#version 2.4
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## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
MAD1L1	8379	hgsc.bcm.edu	37	7	1855715	1855715	+	Silent	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr7:1855715G>A	ENST00000406869.1	-	19	2705	c.2148C>T	c.(2146-2148)acC>acT	p.T716T	MAD1L1_ENST00000402746.1_Silent_p.T624T|MAD1L1_ENST00000399654.2_Silent_p.T716T|MAD1L1_ENST00000265854.7_Silent_p.T716T			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)	716					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|regulation of metaphase plate congression (GO:0090235)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle (GO:0005819)				central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(5)	36		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		GCTACGCCACGGTCTGGCGGC	0.692																																																	0			7											21.0	27.0	25.0					7																	1855715		2055	4208	6263	1822241	SO:0001819	synonymous_variant	8379			U33822	CCDS43539.1	7p22	2013-01-17	2001-11-28		ENSG00000002822	ENSG00000002822			6762	protein-coding gene	gene with protein product		602686	"""MAD1 (mitotic arrest deficient, yeast, homolog)-like 1"""			10049595, 9546394	Standard	XM_005249876		Approved	HsMAD1, TXBP181, MAD1, PIG9, TP53I9	uc003slg.1	Q9Y6D9	OTTHUMG00000151493	ENST00000406869.1:c.2148C>T	7.37:g.1855715G>A			1822241	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Silent	SNP	ENST00000406869.1	37	CCDS43539.1																																																																																				0.692	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550	
GLI3	2737	hgsc.bcm.edu	37	7	42004760	42004760	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr7:42004760G>T	ENST00000395925.3	-	15	3995	c.3911C>A	c.(3910-3912)tCa>tAa	p.S1304*	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	1304			S -> P (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						GCTGCCAGCTGACTCATTTGG	0.637									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																																								0			7											40.0	40.0	40.0					7																	42004760		2203	4300	6503	41971285	SO:0001587	stop_gained	2737	Familial Cancer Database	;		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"""Zinc fingers, C2H2-type"""	4319	protein-coding gene	gene with protein product	"""zinc finger protein GLI3"", ""oncogene GLI3"", ""DNA-binding protein"""	165240	"""Greig cephalopolysyndactyly syndrome"", ""GLI-Kruppel family member GLI3"", ""glioma-associated oncogene family zinc finger 3"""	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.3911C>A	7.37:g.42004760G>T	ENSP00000379258:p.Ser1304*		41971285	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Nonsense_Mutation	SNP	ENST00000395925.3	37	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	G	39	7.552695	0.98355	.	.	ENSG00000106571	ENST00000395925	.	.	.	5.65	2.4	0.29515	.	1.424740	0.03942	N	0.287122	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	6.0097	0.19569	0.2297:0.0:0.5534:0.2169	.	.	.	.	X	1304	.	ENSP00000379258:S1304X	S	-	2	0	GLI3	41971285	0.001000	0.12720	0.161000	0.22692	0.066000	0.16364	0.915000	0.28638	0.721000	0.32231	0.655000	0.94253	TCA		0.637	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	
EGFR	1956	hgsc.bcm.edu	37	7	55259522	55259522	+	Silent	SNP	A	A	G	rs397517130		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr7:55259522A>G	ENST00000275493.2	+	21	2757	c.2580A>G	c.(2578-2580)aaA>aaG	p.K860K	EGFR_ENST00000442591.1_Intron|EGFR-AS1_ENST00000442411.1_RNA|EGFR_ENST00000455089.1_Silent_p.K815K|EGFR_ENST00000454757.2_Silent_p.K807K	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	860	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	GGCTGGCCAAACTGCTGGGTG	0.552		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																													yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	0			7											103.0	97.0	99.0					7																	55259522		2203	4300	6503	55227016	SO:0001819	synonymous_variant	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2580A>G	7.37:g.55259522A>G			55227016	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																				0.552	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
BAZ1B	9031	hgsc.bcm.edu	37	7	72884712	72884712	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr7:72884712G>A	ENST00000339594.4	-	8	3033	c.2695C>T	c.(2695-2697)Cgc>Tgc	p.R899C	BAZ1B_ENST00000404251.1_Missense_Mutation_p.R899C	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	899					cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				GGAGTCCTGCGCATGACTAGT	0.423																																					Esophageal Squamous(112;1167 1561 21085 43672 48228)												0			7											190.0	161.0	171.0					7																	72884712		2203	4300	6503	72522648	SO:0001583	missense	9031			AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"""Zinc fingers, PHD-type"""	961	protein-coding gene	gene with protein product	"""Williams-Beuren syndrome chromosome region 9"", ""Williams-Beuren syndrome chromosome region 10"", ""transcription factor WSTF"""	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.2695C>T	7.37:g.72884712G>A	ENSP00000342434:p.Arg899Cys		72522648	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	37	CCDS5549.1	.	.	.	.	.	.	.	.	.	.	G	19.92	3.915905	0.73098	.	.	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.63580	-0.05;-0.05	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.74030	0.3663	L	0.56769	1.78	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.74003	-0.3804	10	0.46703	T	0.11	-15.9366	12.7402	0.57249	0.0:0.0:0.8358:0.1641	.	899	Q9UIG0	BAZ1B_HUMAN	C	899	ENSP00000342434:R899C;ENSP00000385442:R899C	ENSP00000342434:R899C	R	-	1	0	BAZ1B	72522648	1.000000	0.71417	0.998000	0.56505	0.945000	0.59286	4.869000	0.63028	2.440000	0.82611	0.557000	0.71058	CGC		0.423	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408	
AKAP9	10142	hgsc.bcm.edu	37	7	91726163	91726163	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr7:91726163A>G	ENST00000359028.2	+	41	10127	c.9902A>G	c.(9901-9903)gAg>gGg	p.E3301G	AKAP9_ENST00000358100.2_Missense_Mutation_p.E3247G|AKAP9_ENST00000356239.3_Missense_Mutation_p.E3297G			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3301			E -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			CGAAACTTAGAGCTTCAGGTA	0.433			T	BRAF	papillary thyroid																																			Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	0			7											107.0	104.0	105.0					7																	91726163		2203	4300	6503	91564099	SO:0001583	missense	10142			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.9902A>G	7.37:g.91726163A>G	ENSP00000351922:p.Glu3301Gly		91564099	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	A	15.36	2.811806	0.50527	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	T;T;T;T	0.05580	3.52;3.52;3.59;3.42	5.56	3.21	0.36854	.	0.170707	0.28192	N	0.016253	T	0.06416	0.0165	L	0.42245	1.32	0.40521	D	0.98083	B;B;B;B;B	0.30542	0.284;0.197;0.125;0.197;0.197	B;B;B;B;B	0.30251	0.113;0.09;0.041;0.09;0.09	T	0.37009	-0.9724	10	0.33141	T	0.24	.	9.4705	0.38839	0.8543:0.0:0.1457:0.0	.	572;3301;3301;3297;3289	B3KQF9;Q99996-6;Q99996;Q99996-2;Q99996-3	.;.;AKAP9_HUMAN;.;.	G	3297;3301;3247;3301;1143	ENSP00000348573:E3297G;ENSP00000351922:E3301G;ENSP00000350813:E3247G;ENSP00000378042:E1143G	ENSP00000348573:E3297G	E	+	2	0	AKAP9	91564099	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	4.894000	0.63206	0.496000	0.27904	0.533000	0.62120	GAG		0.433	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
PON3	5446	hgsc.bcm.edu	37	7	94993256	94993256	+	Missense_Mutation	SNP	A	A	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr7:94993256A>T	ENST00000265627.5	-	6	624	c.614T>A	c.(613-615)cTt>cAt	p.L205H	PON3_ENST00000451904.1_Missense_Mutation_p.L205H|PON3_ENST00000427422.1_Missense_Mutation_p.L205H|PON1_ENST00000542556.1_Intron	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	205					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	GCTGTAGAAAAGAACATAAGT	0.443																																																	0			7											182.0	187.0	185.0					7																	94993256		2203	4300	6503	94831192	SO:0001583	missense	5446			L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"""Paraoxonases"""	9206	protein-coding gene	gene with protein product	"""arylesterase 3"""	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.614T>A	7.37:g.94993256A>T	ENSP00000265627:p.Leu205His		94831192	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Missense_Mutation	SNP	ENST00000265627.5	37	CCDS5639.1	.	.	.	.	.	.	.	.	.	.	A	19.69	3.875033	0.72180	.	.	ENSG00000105852	ENST00000265627;ENST00000427422	T;T	0.47177	0.85;0.85	5.27	4.12	0.48240	Six-bladed beta-propeller, TolB-like (1);	0.387835	0.28442	N	0.015332	T	0.61540	0.2355	M	0.66939	2.045	0.09310	N	0.999999	D;D	0.69078	0.997;0.996	P;P	0.61874	0.87;0.895	T	0.55755	-0.8091	10	0.87932	D	0	-2.1494	10.806	0.46518	0.9247:0.0:0.0753:0.0	.	253;205	B4E2I0;Q15166	.;PON3_HUMAN	H	205	ENSP00000265627:L205H;ENSP00000413276:L205H	ENSP00000265627:L205H	L	-	2	0	PON3	94831192	0.999000	0.42202	0.022000	0.16811	0.325000	0.28411	6.606000	0.74159	0.958000	0.37956	0.533000	0.62120	CTT		0.443	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940	
DYNC1I1	1780	hgsc.bcm.edu	37	7	95665046	95665046	+	Missense_Mutation	SNP	C	C	T	rs551953723		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr7:95665046C>T	ENST00000324972.6	+	13	1590	c.1397C>T	c.(1396-1398)aCg>aTg	p.T466M	DYNC1I1_ENST00000359388.4_Missense_Mutation_p.T429M|DYNC1I1_ENST00000497626.1_3'UTR|DYNC1I1_ENST00000537881.1_Missense_Mutation_p.T429M|DYNC1I1_ENST00000437599.1_Missense_Mutation_p.T446M|DYNC1I1_ENST00000457059.1_Missense_Mutation_p.T449M|DYNC1I1_ENST00000447467.2_Missense_Mutation_p.T449M	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	466					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|metabolic process (GO:0008152)|vesicle transport along microtubule (GO:0047496)	cytoplasmic dynein complex (GO:0005868)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)|spectrin binding (GO:0030507)			NS(2)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(27)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	54	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			ACAGTCTACACGGCTTGTCGT	0.448													C|||	1	0.000199681	0.0	0.0	5008	,	,		22007	0.0		0.001	False		,,,				2504	0.0																0			7											344.0	281.0	302.0					7																	95665046		2203	4300	6503	95502982	SO:0001583	missense	1780			AF063228	CCDS5644.1, CCDS47645.1, CCDS47646.1, CCDS64718.1	7q21.3-q22.1	2013-01-18	2005-11-24	2005-11-24	ENSG00000158560	ENSG00000158560		"""Cytoplasmic dyneins"", ""WD repeat domain containing"""	2963	protein-coding gene	gene with protein product		603772	"""dynein, cytoplasmic, intermediate polypeptide 1"""	DNCI1		10049579, 16260502	Standard	NM_004411		Approved	DNCIC1	uc003uoc.4	O14576	OTTHUMG00000153983	ENST00000324972.6:c.1397C>T	7.37:g.95665046C>T	ENSP00000320130:p.Thr466Met		95502982	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Missense_Mutation	SNP	ENST00000324972.6	37	CCDS5644.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.922266	0.33908	.	.	ENSG00000158560	ENST00000447467;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000457059	T;T;T;T;T;T	0.06218	3.33;3.33;3.33;3.33;3.33;3.33	5.1	5.1	0.69264	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.050263	0.85682	D	0.000000	T	0.08313	0.0207	L	0.52364	1.645	0.58432	D	0.999992	P;P;P;B;P	0.45672	0.624;0.741;0.741;0.425;0.864	B;B;B;B;B	0.35182	0.097;0.197;0.197;0.097;0.133	T	0.13548	-1.0505	10	0.49607	T	0.09	-20.8872	19.0933	0.93238	0.0:1.0:0.0:0.0	.	449;446;449;466;429	Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3	.;.;.;DC1I1_HUMAN;.	M	449;466;429;446;429;449	ENSP00000392337:T449M;ENSP00000320130:T466M;ENSP00000438377:T429M;ENSP00000398118:T446M;ENSP00000352348:T429M;ENSP00000412444:T449M	ENSP00000320130:T466M	T	+	2	0	DYNC1I1	95502982	0.997000	0.39634	0.971000	0.41717	0.492000	0.33523	3.645000	0.54389	2.830000	0.97506	0.585000	0.79938	ACG		0.448	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411	
PPP1R3A	5506	hgsc.bcm.edu	37	7	113518303	113518303	+	Silent	SNP	C	C	T	rs150965727		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr7:113518303C>T	ENST00000284601.3	-	4	2912	c.2844G>A	c.(2842-2844)acG>acA	p.T948T		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	948					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)		p.T948T(3)		NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						TTTCTGATTTCGTAGAAATAG	0.378																																																	3	Substitution - coding silent(3)	skin(3)	7						C		0,4406		0,0,2203	86.0	86.0	86.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2844	-8.2	0.0	7	dbSNP_134	86	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PPP1R3A	NM_002711.3		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		948/1123	113518303	1,13003	2203	4299	6502	113305539	SO:0001819	synonymous_variant	5506			AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9291	protein-coding gene	gene with protein product	"""glycogen-associated regulatory subunit of protein phosphatase-1"", ""protein phosphatase 1 regulatory subunit GM"""	600917	"""protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)"", ""protein phosphatase 1, regulatory (inhibitor) subunit 3A"""	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.2844G>A	7.37:g.113518303C>T			113305539	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Silent	SNP	ENST00000284601.3	37	CCDS5759.1																																																																																				0.378	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711	
PSMF1	9491	hgsc.bcm.edu	37	20	1115856	1115856	+	Missense_Mutation	SNP	G	G	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr20:1115856G>T	ENST00000335877.6	+	4	634	c.458G>T	c.(457-459)aGt>aTt	p.S153I	PSMF1_ENST00000484891.1_3'UTR|PSMF1_ENST00000333082.3_Missense_Mutation_p.S153I|PSMF1_ENST00000381898.4_Missense_Mutation_p.S65I|PSMF1_ENST00000438768.2_Intron|PSMF1_ENST00000246015.4_Missense_Mutation_p.S153I	NM_006814.3	NP_006805.2	Q92530	PSMF1_HUMAN	proteasome (prosome, macropain) inhibitor subunit 1 (PI31)	153					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteasomal protein catabolic process (GO:1901799)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome core complex (GO:0005839)	endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)			endometrium(1)|kidney(1)|large_intestine(3)|lung(8)	13						AATGTAAGCAGTCCCCACCGG	0.572																																																	0			20											116.0	102.0	107.0					20																	1115856		2203	4300	6503	1063856	SO:0001583	missense	9491			D88378	CCDS13010.1	20p13	2008-07-02			ENSG00000125818	ENSG00000125818		"""Proteasome (prosome, macropain) subunits"""	9571	protein-coding gene	gene with protein product	"""proteasome inhibitor hP131 subunit"""					10363639	Standard	NM_006814		Approved	PI31	uc002wen.4	Q92530	OTTHUMG00000031656	ENST00000335877.6:c.458G>T	20.37:g.1115856G>T	ENSP00000338039:p.Ser153Ile		1063856	A0AVQ9|D3DVW3|Q9H4I1	Missense_Mutation	SNP	ENST00000335877.6	37	CCDS13010.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.610|6.610	0.481018|0.481018	0.12581|0.12581	.|.	.|.	ENSG00000125818|ENSG00000125818	ENST00000435720|ENST00000333082;ENST00000381898;ENST00000381899;ENST00000454500;ENST00000246015;ENST00000335877	.|T;T;T;T;T	.|0.47177	.|1.34;0.85;1.38;1.33;1.34	5.22|5.22	2.09|2.09	0.27110|0.27110	.|.	.|0.522992	.|0.21889	.|N	.|0.067607	T|T	0.36110|0.36110	0.0955|0.0955	L|L	0.47716|0.47716	1.5|1.5	0.33144|0.33144	D|D	0.544744|0.544744	.|P;B;B;B	.|0.37636	.|0.603;0.119;0.201;0.257	.|B;B;B;B	.|0.37304	.|0.246;0.055;0.03;0.075	T|T	0.48127|0.48127	-0.9062|-0.9062	5|10	.|0.52906	.|T	.|0.07	0.1591|0.1591	5.0394|5.0394	0.14451|0.14451	0.2412:0.1597:0.5991:0.0|0.2412:0.1597:0.5991:0.0	.|.	.|65;65;153;153	.|F5H4Z3;B4DUJ0;Q5QPM7;Q92530	.|.;.;.;PSMF1_HUMAN	H|I	12|153;65;153;65;153;153	.|ENSP00000327704:S153I;ENSP00000371323:S65I;ENSP00000371324:S153I;ENSP00000246015:S153I;ENSP00000338039:S153I	.|ENSP00000246015:S153I	Q|S	+|+	3|2	2|0	PSMF1|PSMF1	1063856|1063856	0.995000|0.995000	0.38212|0.38212	0.969000|0.969000	0.41365|0.41365	0.032000|0.032000	0.12392|0.12392	2.256000|2.256000	0.43231|0.43231	0.750000|0.750000	0.32877|0.32877	-0.157000|-0.157000	0.13467|0.13467	CAG|AGT		0.572	PSMF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077504.2	NM_178578	
SEL1L2	80343	hgsc.bcm.edu	37	20	13867033	13867033	+	Silent	SNP	C	C	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr20:13867033C>A	ENST00000284951.5	-	9	875	c.801G>T	c.(799-801)acG>acT	p.T267T	SEL1L2_ENST00000486903.1_5'UTR|SEL1L2_ENST00000378072.5_Silent_p.T267T			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	267						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						CAGGTCTTTCCGTTAGTCTCA	0.373																																																	0			20											133.0	122.0	125.0					20																	13867033		1837	4094	5931	13815033	SO:0001819	synonymous_variant	80343			AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"""chromosome 20 open reading frame 50"""	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.801G>T	20.37:g.13867033C>A			13815033	B4DXX5	Silent	SNP	ENST00000284951.5	37																																																																																					0.373	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229	
CTNNBL1	56259	hgsc.bcm.edu	37	20	36470761	36470761	+	Silent	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr20:36470761G>A	ENST00000361383.6	+	13	1449	c.1332G>A	c.(1330-1332)ttG>ttA	p.L444L	CTNNBL1_ENST00000373469.1_Silent_p.L192L|CTNNBL1_ENST00000473857.1_3'UTR|CTNNBL1_ENST00000405275.2_Silent_p.L417L|CTNNBL1_ENST00000373473.1_Silent_p.L257L	NM_030877.3	NP_110517.2	Q8WYA6	CTBL1_HUMAN	catenin, beta like 1	444					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|positive regulation of apoptotic process (GO:0043065)|RNA splicing (GO:0008380)|somatic diversification of immunoglobulins (GO:0016445)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(6)|lung(6)|ovary(3)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				TAATGGAGTTGCATTTTAAAT	0.453																																					Ovarian(184;582 2038 3273 4106 42608)												0			20											161.0	128.0	139.0					20																	36470761		2203	4300	6503	35904175	SO:0001819	synonymous_variant	56259			AL023804	CCDS13298.1	20q11.23-q12	2011-06-03	2002-05-27	2002-05-31	ENSG00000132792	ENSG00000132792			15879	protein-coding gene	gene with protein product	"""nuclear associated protein"""	611537	"""chromosome 20 open reading frame 33"""	C20orf33		12659813, 21385873	Standard	NM_030877		Approved	FLJ21108, P14L, P14, NAP, NYD-SP19	uc021wdj.1	Q8WYA6	OTTHUMG00000032428	ENST00000361383.6:c.1332G>A	20.37:g.36470761G>A			35904175	B4DE16|Q0VAL9|Q0VAM0|Q53HI8|Q5JWZ2|Q5JWZ3|Q5JWZ7|Q5JWZ8|Q8N454|Q8NCL2|Q8TBD6|Q96KD2|Q9H7A5|Q9NQF9|Q9NTX0|Q9Y3M7	Silent	SNP	ENST00000361383.6	37	CCDS13298.1																																																																																				0.453	CTNNBL1-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079125.1	NM_030877	
ZNF217	7764	hgsc.bcm.edu	37	20	52192707	52192707	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr20:52192707C>T	ENST00000371471.2	-	4	3021	c.2596G>A	c.(2596-2598)Gta>Ata	p.V866I	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Missense_Mutation_p.V866I			O75362	ZN217_HUMAN	zinc finger protein 217	866					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			GAAGGAGCTACTGGAAGAGGT	0.532																																																	0			20											88.0	84.0	85.0					20																	52192707		2203	4300	6503	51626114	SO:0001583	missense	7764			AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.2596G>A	20.37:g.52192707C>T	ENSP00000360526:p.Val866Ile		51626114	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	C	6.156	0.397054	0.11638	.	.	ENSG00000171940	ENST00000371471;ENST00000302342;ENST00000395971	T;T	0.07567	3.18;3.18	5.0	3.83	0.44106	.	1.781150	0.03171	N	0.170766	T	0.06416	0.0165	N	0.14661	0.345	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.25222	-1.0138	10	0.11485	T	0.65	0.3058	10.1998	0.43075	0.0:0.8466:0.0:0.1534	.	866	O75362	ZN217_HUMAN	I	866;866;26	ENSP00000360526:V866I;ENSP00000304308:V866I	ENSP00000304308:V866I	V	-	1	0	ZNF217	51626114	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	-0.035000	0.12205	2.304000	0.77564	0.650000	0.86243	GTA		0.532	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
PSMA3	5684	hgsc.bcm.edu	37	14	58718854	58718854	+	Missense_Mutation	SNP	G	G	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr14:58718854G>T	ENST00000216455.4	+	3	212	c.122G>T	c.(121-123)aGa>aTa	p.R41I	PSMA3_ENST00000412908.2_Missense_Mutation_p.R41I|PSMA3_ENST00000557508.1_5'UTR	NM_002788.3|NM_152132.2	NP_002779.1|NP_687033.1	P25788	PSA3_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 3	41					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	threonine-type endopeptidase activity (GO:0004298)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(2)	12						ATTGGAATCAGATGCAAAGAT	0.294																																																	0			14											118.0	118.0	118.0					14																	58718854		2203	4300	6503	57788607	SO:0001583	missense	5684				CCDS9731.1, CCDS45113.1	14q23	2008-08-29			ENSG00000100567	ENSG00000100567		"""Proteasome (prosome, macropain) subunits"""	9532	protein-coding gene	gene with protein product		176843				2025653, 8811196	Standard	NM_002788		Approved	HC8	uc001xdj.2	P25788	OTTHUMG00000140319	ENST00000216455.4:c.122G>T	14.37:g.58718854G>T	ENSP00000216455:p.Arg41Ile		57788607	B2RCK6|Q86U83|Q8N1D8|Q9BS70	Missense_Mutation	SNP	ENST00000216455.4	37	CCDS9731.1	.	.	.	.	.	.	.	.	.	.	G	17.56	3.419072	0.62622	.	.	ENSG00000100567	ENST00000216455;ENST00000412908	T;T	0.24350	1.86;1.86	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.61388	0.2343	M	0.90309	3.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.986;0.992	T	0.68815	-0.5309	10	0.87932	D	0	-18.4014	19.7578	0.96301	0.0:0.0:1.0:0.0	.	41;41	P25788-2;P25788	.;PSA3_HUMAN	I	41	ENSP00000216455:R41I;ENSP00000390491:R41I	ENSP00000216455:R41I	R	+	2	0	PSMA3	57788607	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.420000	0.97426	2.748000	0.94277	0.655000	0.94253	AGA		0.294	PSMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276923.1	NM_002788	
KCNH5	27133	hgsc.bcm.edu	37	14	63174536	63174536	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr14:63174536T>C	ENST00000322893.7	-	11	2925	c.2657A>G	c.(2656-2658)gAg>gGg	p.E886G	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	886					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		GGGACTGTGCTCTAGCGGACT	0.502																																																	0			14											128.0	115.0	119.0					14																	63174536		2203	4300	6503	62244289	SO:0001583	missense	27133			U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.2657A>G	14.37:g.63174536T>C	ENSP00000321427:p.Glu886Gly		62244289	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	T	11.04	1.522810	0.27211	.	.	ENSG00000140015	ENST00000322893	D	0.99060	-5.38	5.44	5.44	0.79542	.	0.278712	0.35772	N	0.002984	D	0.96275	0.8785	N	0.14661	0.345	0.80722	D	1	B	0.22683	0.073	B	0.24701	0.055	D	0.94546	0.7749	10	0.30854	T	0.27	.	15.6661	0.77230	0.0:0.0:0.0:1.0	.	886	Q8NCM2	KCNH5_HUMAN	G	886	ENSP00000321427:E886G	ENSP00000321427:E886G	E	-	2	0	KCNH5	62244289	1.000000	0.71417	0.998000	0.56505	0.529000	0.34654	4.510000	0.60455	2.285000	0.76669	0.533000	0.62120	GAG		0.502	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318	
ESRRB	2103	hgsc.bcm.edu	37	14	76905829	76905829	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr14:76905829T>C	ENST00000509242.1	+	3	231	c.133T>C	c.(133-135)Ttt>Ctt	p.F45L	ESRRB_ENST00000380887.2_Missense_Mutation_p.F45L|ESRRB_ENST00000556177.1_Missense_Mutation_p.F45L|ESRRB_ENST00000507951.1_3'UTR|ESRRB_ENST00000261532.7_Missense_Mutation_p.F45L	NM_004452.3	NP_004443.3	O95718	ERR2_HUMAN	estrogen-related receptor beta	45					gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|trophectodermal cell proliferation (GO:0001834)|trophectodermal cellular morphogenesis (GO:0001831)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(234;0.0213)		CAGCGGCGGCTTTGGCCTGGC	0.692																																																	0			14											22.0	25.0	24.0					14																	76905829		2194	4280	6474	75975582	SO:0001583	missense	2103			X51417	CCDS9850.1, CCDS9850.2	14q24.3	2013-01-16				ENSG00000119715		"""Nuclear hormone receptors"""	3473	protein-coding gene	gene with protein product		602167	"""deafness, autosomal recessive 35"""	ESRL2, DFNB35		3267207, 9344655, 18179891	Standard	NM_004452		Approved	ERR2, ERRbeta, NR3B2, ERRb	uc001xsr.3	O95718		ENST00000509242.1:c.133T>C	14.37:g.76905829T>C	ENSP00000422488:p.Phe45Leu		75975582	A2VDJ2|B6ZGU4|Q5F0P7|Q5F0P8|Q9HCB4	Missense_Mutation	SNP	ENST00000509242.1	37	CCDS9850.2	.	.	.	.	.	.	.	.	.	.	T	21.8	4.198223	0.79015	.	.	ENSG00000119715	ENST00000512784;ENST00000509242;ENST00000556177;ENST00000380887;ENST00000261532	D;D;D;D;D	0.92348	-3.01;-3.02;-3.0;-3.02;-2.99	5.13	5.13	0.70059	.	0.056855	0.64402	D	0.000001	D	0.84156	0.5410	N	0.08118	0	0.45806	D	0.998686	B;B	0.29552	0.128;0.248	B;B	0.29524	0.103;0.103	D	0.84119	0.0405	10	0.72032	D	0.01	.	14.9565	0.71116	0.0:0.0:0.0:1.0	.	45;50	Q5F0P7;E7EWD9	.;.	L	50;45;45;45;45	ENSP00000424992:F50L;ENSP00000422488:F45L;ENSP00000451658:F45L;ENSP00000370270:F45L;ENSP00000261532:F45L	ENSP00000261532:F45L	F	+	1	0	ESRRB	75975582	1.000000	0.71417	0.969000	0.41365	0.897000	0.52465	8.000000	0.88501	1.937000	0.56155	0.533000	0.62120	TTT		0.692	ESRRB-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360663.1		
TMEM63C	57156	hgsc.bcm.edu	37	14	77714714	77714714	+	Silent	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr14:77714714C>T	ENST00000298351.4	+	19	1770	c.1626C>T	c.(1624-1626)ggC>ggT	p.G542G		NM_020431.2	NP_065164.2	Q9P1W3	CSC1_HUMAN	transmembrane protein 63C	542					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)	integral component of membrane (GO:0016021)	calcium activated cation channel activity (GO:0005227)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(1)	23			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)		CAGACAACGGCGCCTTCTTTG	0.567																																																	0			14											49.0	49.0	49.0					14																	77714714		2201	4299	6500	76784467	SO:0001819	synonymous_variant	57156				CCDS45141.1	14q24.3	2014-05-30	2005-07-25	2005-07-25	ENSG00000165548	ENSG00000165548			23787	protein-coding gene	gene with protein product	"""calcium permeable stress-gated cation channel 1 homolog (Arabidopsis)"""		"""chromosome 14 open reading frame 171"""	C14orf171		24503647	Standard	NM_020431		Approved	DKFZp434P0111, CSC1, hsCSC1	uc001xtf.2	Q9P1W3	OTTHUMG00000171557	ENST00000298351.4:c.1626C>T	14.37:g.77714714C>T			76784467	B2RN22|B3KWJ5|Q86TS3|Q86TS4|Q9NSQ4|Q9P1W1	Silent	SNP	ENST00000298351.4	37	CCDS45141.1																																																																																				0.567	TMEM63C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414193.1		
STK11	6794	hgsc.bcm.edu	37	19	1223020	1223020	+	Silent	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:1223020A>G	ENST00000326873.7	+	8	2130	c.957A>G	c.(955-957)ccA>ccG	p.P319P		NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	319					activation of protein kinase activity (GO:0032147)|anoikis (GO:0043276)|autophagy (GO:0006914)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|energy reserve metabolic process (GO:0006112)|establishment of cell polarity (GO:0030010)|glucose homeostasis (GO:0042593)|Golgi localization (GO:0051645)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of protein kinase B signaling (GO:0051896)|regulation of Wnt signaling pathway (GO:0030111)|response to glucagon (GO:0033762)|response to ionizing radiation (GO:0010212)|response to lipid (GO:0033993)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|T cell receptor signaling pathway (GO:0050852)|TCR signalosome assembly (GO:0036399)|tissue homeostasis (GO:0001894)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|TCR signalosome (GO:0036398)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|p53 binding (GO:0002039)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.0?(20)|p.V320fs*16(1)		biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGAAGCACCAGTGCCCATCC	0.652		14	"""D, Mis, N, F, S"""		"""NSCLC, pancreatic"""	"""jejunal harmartoma, ovarian, testicular, pancreatic"""			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)																													yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"""E, M, O"""	21	Whole gene deletion(20)|Complex - frameshift(1)	cervix(15)|lung(2)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)	19	GRCh37	CX012582	STK11	X							34.0	41.0	39.0					19																	1223020		2095	4216	6311	1174020	SO:0001819	synonymous_variant	6794	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	U63333	CCDS45896.1	19p13.3	2014-09-17	2005-12-13			ENSG00000118046			11389	protein-coding gene	gene with protein product	"""polarization-related protein LKB1"""	602216	"""serine/threonine kinase 11 (Peutz-Jeghers syndrome)"""			9425897	Standard	XM_005259617		Approved	PJS, LKB1	uc002lrl.1	Q15831		ENST00000326873.7:c.957A>G	19.37:g.1223020A>G			1174020	B2RBX7|E7EW76	Silent	SNP	ENST00000326873.7	37	CCDS45896.1																																																																																				0.652	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455	
KLHL26	55295	hgsc.bcm.edu	37	19	18779181	18779181	+	Missense_Mutation	SNP	C	C	T	rs148560244	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:18779181C>T	ENST00000300976.4	+	3	1064	c.974C>T	c.(973-975)tCg>tTg	p.S325L	KLHL26_ENST00000599006.1_Intron	NM_018316.1	NP_060786.1	Q53HC5	KLH26_HUMAN	kelch-like family member 26	325										breast(1)|central_nervous_system(1)|kidney(1)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						AGCGACCGCTCGGTCAGCAGC	0.692													C|||	3	0.000599042	0.0023	0.0	5008	,	,		12999	0.0		0.0	False		,,,				2504	0.0																0			19						C	LEU/SER	4,4392		0,4,2194	16.0	16.0	16.0		974	4.0	0.0	19	dbSNP_134	16	0,8568		0,0,4284	no	missense	KLHL26	NM_018316.1	145	0,4,6478	TT,TC,CC		0.0,0.091,0.0309	benign	325/616	18779181	4,12960	2198	4284	6482	18640181	SO:0001583	missense	55295				CCDS12384.1	19p13.11	2013-10-15	2013-02-22		ENSG00000167487	ENSG00000167487		"""Kelch-like"", ""BTB/POZ domain containing"""	25623	protein-coding gene	gene with protein product			"""kelch-like 26 (Drosophila)"""				Standard	XM_006722785		Approved		uc002njz.1	Q53HC5	OTTHUMG00000183114	ENST00000300976.4:c.974C>T	19.37:g.18779181C>T	ENSP00000300976:p.Ser325Leu		18640181	Q8TAP0|Q9NUX3	Missense_Mutation	SNP	ENST00000300976.4	37	CCDS12384.1	.	.	.	.	.	.	.	.	.	.	C	10.48	1.362170	0.24684	9.1E-4	0.0	ENSG00000167487	ENST00000300976	T	0.75821	-0.97	5.04	3.98	0.46160	Galactose oxidase, beta-propeller (1);	0.401657	0.26467	N	0.024220	T	0.55337	0.1914	N	0.12887	0.27	0.20563	N	0.99989	B	0.24576	0.106	B	0.17433	0.018	T	0.34625	-0.9821	9	.	.	.	.	14.3318	0.66561	0.0:0.8504:0.1496:0.0	.	325	Q53HC5	KLH26_HUMAN	L	325	ENSP00000300976:S325L	.	S	+	2	0	KLHL26	18640181	0.670000	0.27512	0.007000	0.13788	0.737000	0.42083	3.715000	0.54897	1.078000	0.41014	0.591000	0.81541	TCG		0.692	KLHL26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465145.1	NM_018316	
CEP89	84902	hgsc.bcm.edu	37	19	33450807	33450807	+	Splice_Site	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:33450807G>A	ENST00000305768.5	-	3	392	c.304C>T	c.(304-306)Cgg>Tgg	p.R102W	CEP89_ENST00000590597.2_Splice_Site_p.R102W	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	102					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						GGTACCTACCGAGGCCTCAGC	0.587																																																	0			19											98.0	79.0	85.0					19																	33450807		2203	4300	6503	38142647	SO:0001630	splice_region_variant	84902			AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.305+1C>T	19.37:g.33450807G>A			38142647	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	.	.	.	.	.	.	.	.	.	.	G	11.27	1.589173	0.28357	.	.	ENSG00000121289	ENST00000305768	T	0.33216	1.42	5.48	3.25	0.37280	.	0.317619	0.28382	N	0.015556	T	0.28200	0.0696	L	0.46157	1.445	0.34322	D	0.686742	B;B	0.22414	0.01;0.069	B;B	0.16289	0.007;0.015	T	0.43097	-0.9412	10	0.62326	D	0.03	-1.7133	14.057	0.64776	0.0:0.5783:0.4217:0.0	.	102;102	Q96ST8-3;Q96ST8	.;CEP89_HUMAN	W	102	ENSP00000306105:R102W	ENSP00000306105:R102W	R	-	1	2	CEP89	38142647	0.935000	0.31712	0.697000	0.30258	0.024000	0.10985	1.735000	0.38176	1.276000	0.44395	0.655000	0.94253	CGG		0.587	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	Missense_Mutation
RYR1	6261	hgsc.bcm.edu	37	19	38968461	38968461	+	Missense_Mutation	SNP	C	C	T	rs200546266		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:38968461C>T	ENST00000359596.3	+	30	4405	c.4405C>T	c.(4405-4407)Cgg>Tgg	p.R1469W	RYR1_ENST00000355481.4_Missense_Mutation_p.R1469W|RYR1_ENST00000360985.3_Missense_Mutation_p.R1469W			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1469	6 X approximate repeats.|B30.2/SPRY 3. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CAGCAAGGTCCGGGTCGTGAC	0.667													C|||	1	0.000199681	0.0	0.0	5008	,	,		14060	0.0		0.001	False		,,,				2504	0.0																0			19						C	TRP/ARG,TRP/ARG	0,4406		0,0,2203	63.0	50.0	55.0		4405,4405	3.3	1.0	19		55	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	RYR1	NM_000540.2,NM_001042723.1	101,101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	1469/5039,1469/5034	38968461	1,13005	2203	4300	6503	43660301	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.4405C>T	19.37:g.38968461C>T	ENSP00000352608:p.Arg1469Trp		43660301	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.64	2.894071	0.52121	0.0	1.16E-4	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.71103	-0.54;-0.54;-0.54	5.41	3.26	0.37387	SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.64402	U	0.000018	T	0.82130	0.4970	M	0.84326	2.69	0.47584	D	0.999464	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.82552	-0.0400	10	0.72032	D	0.01	.	7.7965	0.29150	0.143:0.7251:0.0:0.1319	.	1469;1469	P21817-2;P21817	.;RYR1_HUMAN	W	1469	ENSP00000352608:R1469W;ENSP00000347667:R1469W;ENSP00000354254:R1469W	ENSP00000347667:R1469W	R	+	1	2	RYR1	43660301	1.000000	0.71417	1.000000	0.80357	0.577000	0.36160	2.478000	0.45189	1.271000	0.44313	0.313000	0.20887	CGG		0.667	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
GSK3A	2931	hgsc.bcm.edu	37	19	42735003	42735003	+	Silent	SNP	C	C	T	rs372575967	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:42735003C>T	ENST00000222330.3	-	11	1522	c.1395G>A	c.(1393-1395)ccG>ccA	p.P465P	GSK3A_ENST00000398249.4_Silent_p.P383P	NM_019884.2	NP_063937.2	P49840	GSK3A_HUMAN	glycogen synthase kinase 3 alpha	465					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cardiac left ventricle morphogenesis (GO:0003214)|cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|cellular response to interleukin-3 (GO:0036016)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|endoplasmic reticulum unfolded protein response (GO:0030968)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transferase activity (GO:0051348)|negative regulation of type B pancreatic cell development (GO:2000077)|negative regulation of UDP-glucose catabolic process (GO:0010905)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of heart contraction (GO:0045823)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein phosphorylation (GO:0006468)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of systemic arterial blood pressure (GO:0003073)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cytosol (GO:0005829)	ATP binding (GO:0005524)|protein kinase A catalytic subunit binding (GO:0034236)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(3)|large_intestine(3)|lung(6)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	19		Prostate(69;0.00682)				CTGAGCTGGTCGGAGTCTCAG	0.567													C|||	23	0.00459265	0.0	0.0	5008	,	,		14554	0.0		0.0	False		,,,				2504	0.0235																0			19											84.0	68.0	74.0					19																	42735003		2198	4288	6486	47426843	SO:0001819	synonymous_variant	2931				CCDS12599.1	19q13	2008-02-15			ENSG00000105723	ENSG00000105723			4616	protein-coding gene	gene with protein product		606784				9809441	Standard	NM_019884		Approved		uc002otb.1	P49840	OTTHUMG00000150722	ENST00000222330.3:c.1395G>A	19.37:g.42735003C>T			47426843	O14959	Silent	SNP	ENST00000222330.3	37	CCDS12599.1																																																																																				0.567	GSK3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319782.1		
LIPE	3991	hgsc.bcm.edu	37	19	42930864	42930864	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:42930864T>C	ENST00000244289.4	-	1	714	c.438A>G	c.(436-438)ccA>ccG	p.P146P	LIPE-AS1_ENST00000593740.2_RNA|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000594688.1_RNA|CTB-50E14.4_ENST00000596781.1_RNA|LIPE-AS1_ENST00000457234.2_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	146			P -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|P -> S (in dbSNP:rs34348028). {ECO:0000269|Ref.3}.		cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)			breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				GAGCTGGAGGTGGCTCTCCTG	0.562																																																	0			19											87.0	87.0	87.0					19																	42930864		2203	4300	6503	47622704	SO:0001819	synonymous_variant	3991			L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.438A>G	19.37:g.42930864T>C			47622704	Q3LRT2|Q6NSL7	Silent	SNP	ENST00000244289.4	37	CCDS12607.1																																																																																				0.562	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357	
PLA2G4C	8605	hgsc.bcm.edu	37	19	48558305	48558305	+	Splice_Site	SNP	G	G	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:48558305G>T	ENST00000599921.1	-	15	1616	c.1259C>A	c.(1258-1260)aCc>aAc	p.T420N	PLA2G4C_ENST00000599111.1_Splice_Site_p.T430N|PLA2G4C_ENST00000354276.3_Splice_Site_p.T420N|PLA2G4C_ENST00000596510.1_5'UTR|PLA2G4C_ENST00000413144.2_Splice_Site_p.T420N			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	420	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		AGCCCGGATGGTCTGAGAAGG	0.587																																																	0			19											60.0	60.0	60.0					19																	48558305		2203	4300	6503	53250117	SO:0001630	splice_region_variant	8605			AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.1258-1C>A	19.37:g.48558305G>T			53250117	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	37	CCDS12710.1	.	.	.	.	.	.	.	.	.	.	G	18.60	3.658437	0.67586	.	.	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.12361	2.69;2.69	3.19	3.19	0.36642	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.084168	0.46145	U	0.000317	T	0.30792	0.0776	M	0.65498	2.005	0.34102	D	0.661925	D;D	0.89917	0.999;1.0	D;D	0.87578	0.993;0.998	T	0.39901	-0.9591	10	0.35671	T	0.21	-17.8502	10.1982	0.43067	0.0:0.0:1.0:0.0	.	430;420	B4DI40;Q9UP65	.;PA24C_HUMAN	N	420	ENSP00000346228:T420N;ENSP00000400036:T420N	ENSP00000346228:T420N	T	-	2	0	PLA2G4C	53250117	1.000000	0.71417	0.813000	0.32504	0.488000	0.33401	2.704000	0.47118	1.481000	0.48307	0.411000	0.27672	ACC		0.587	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1		Missense_Mutation
KLK10	5655	hgsc.bcm.edu	37	19	51518084	51518084	+	Nonsense_Mutation	SNP	C	C	T	rs78258028	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:51518084C>T	ENST00000309958.3	-	6	1021	c.803G>A	c.(802-804)tGg>tAg	p.W268*	KLK10_ENST00000391805.1_Nonsense_Mutation_p.W268*|KLK10_ENST00000358789.3_Nonsense_Mutation_p.W268*|CTB-147C22.9_ENST00000594512.1_RNA|CTC-518B2.12_ENST00000596286.1_RNA	NM_002776.4	NP_002767.2	O43240	KLK10_HUMAN	kallikrein-related peptidase 10	268	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00885)		TTTATTGATCCAGGACATGTA	0.537													C|||	6	0.00119808	0.0	0.0	5008	,	,		20674	0.005		0.0	False		,,,				2504	0.001																0			19											146.0	133.0	138.0					19																	51518084		2203	4300	6503	56209896	SO:0001587	stop_gained	5655			AF024605	CCDS12817.1	19q13	2011-03-07	2006-10-27			ENSG00000129451		"""Kallikreins"""	6358	protein-coding gene	gene with protein product		602673	"""kallikrein 10"""	PRSSL1		8764136, 9533035, 16800724, 16800723, 10675891	Standard	NM_145888		Approved	NES1	uc002pva.3	O43240		ENST00000309958.3:c.803G>A	19.37:g.51518084C>T	ENSP00000311746:p.Trp268*		56209896	A6NC12|Q53YL3|Q99920|Q9GZW9	Nonsense_Mutation	SNP	ENST00000309958.3	37	CCDS12817.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	c	20.2	3.954908	0.73902	.	.	ENSG00000129451	ENST00000391805;ENST00000309958;ENST00000358789	.	.	.	4.66	4.66	0.58398	.	.	.	.	.	.	.	.	.	.	.	0.52099	D	0.99994	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.4099	0.74911	0.0:1.0:0.0:0.0	.	.	.	.	X	268	.	ENSP00000311746:W268X	W	-	2	0	KLK10	56209896	1.000000	0.71417	0.942000	0.38095	0.047000	0.14425	7.187000	0.77730	2.318000	0.78349	0.313000	0.20887	TGG		0.537	KLK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464337.2	NM_002776	
IGLON5	402665	hgsc.bcm.edu	37	19	51827033	51827033	+	Silent	SNP	C	C	T	rs200499741	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:51827033C>T	ENST00000270642.8	+	3	276	c.276C>T	c.(274-276)ccC>ccT	p.P92P		NM_001101372.1	NP_001094842.1	A6NGN9	IGLO5_HUMAN	IgLON family member 5	92	Ig-like C2-type 1.					extracellular region (GO:0005576)				large_intestine(5)|lung(6)|prostate(1)	12						TCAACACCCCCGAGGAGTTCT	0.657													C|||	16	0.00319489	0.0	0.0014	5008	,	,		15965	0.0		0.0	False		,,,				2504	0.0153																0			19											34.0	41.0	39.0					19																	51827033		1975	4147	6122	56518845	SO:0001819	synonymous_variant	402665				CCDS46158.1	19q13.33	2013-01-29			ENSG00000142549	ENSG00000142549		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	34550	protein-coding gene	gene with protein product							Standard	NM_001101372		Approved	LOC402665	uc002pwc.2	A6NGN9	OTTHUMG00000154422	ENST00000270642.8:c.276C>T	19.37:g.51827033C>T			56518845		Silent	SNP	ENST00000270642.8	37	CCDS46158.1																																																																																				0.657	IGLON5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335149.1	NM_001101372	
NLRP12	91662	hgsc.bcm.edu	37	19	54314533	54314533	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:54314533T>C	ENST00000324134.6	-	3	548	c.380A>G	c.(379-381)gAa>gGa	p.E127G	NLRP12_ENST00000535162.1_Missense_Mutation_p.E127G|NLRP12_ENST00000345770.5_Missense_Mutation_p.E127G|NLRP12_ENST00000354278.3_Missense_Mutation_p.E127G|NLRP12_ENST00000391772.1_Missense_Mutation_p.E127G|NLRP12_ENST00000351894.4_Missense_Mutation_p.E127G|NLRP12_ENST00000391773.1_Missense_Mutation_p.E127G|NLRP12_ENST00000391775.3_Missense_Mutation_p.E127G	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	127					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		CCTGTAGGTTTCCTGGGGATC	0.542																																																	0			19											73.0	72.0	72.0					19																	54314533		2202	4295	6497	59006345	SO:0001583	missense	91662			AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"""Nucleotide-binding domain and leucine rich repeat containing"""	22938	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"""	609648	"""NACHT, leucine rich repeat and PYD containing 12"""	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.380A>G	19.37:g.54314533T>C	ENSP00000319377:p.Glu127Gly		59006345	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	37	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	T	11.14	1.551798	0.27739	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	T;T;T;T;T;T;T	0.75154	-0.84;-0.87;-0.9;-0.91;-0.89;-0.84;-0.88	4.47	2.31	0.28768	.	0.703660	0.12215	N	0.488905	T	0.64951	0.2645	L	0.57536	1.79	0.09310	N	1	B;P;P;P	0.40144	0.255;0.651;0.651;0.704	B;B;B;B	0.35859	0.104;0.15;0.212;0.197	T	0.55289	-0.8164	10	0.48119	T	0.1	.	4.8331	0.13451	0.3279:0.0:0.1697:0.5023	.	127;127;127;127	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	G	127	ENSP00000319377:E127G;ENSP00000438030:E127G;ENSP00000340473:E127G;ENSP00000346231:E127G;ENSP00000375655:E127G;ENSP00000375653:E127G;ENSP00000375652:E127G	ENSP00000319377:E127G	E	-	2	0	NLRP12	59006345	0.003000	0.15002	0.001000	0.08648	0.228000	0.25075	1.300000	0.33436	0.197000	0.20387	0.254000	0.18369	GAA		0.542	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687	
NLRP13	126204	hgsc.bcm.edu	37	19	56443518	56443518	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:56443518G>A	ENST00000342929.3	-	1	159	c.160C>T	c.(160-162)Cgt>Tgt	p.R54C	NLRP13_ENST00000588751.1_Missense_Mutation_p.R54C	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	54	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		CAGGGGATACGCGGGAAGTGC	0.557																																																	0			19											57.0	60.0	59.0					19																	56443518		2203	4300	6503	61135330	SO:0001583	missense	126204			AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"""Nucleotide-binding domain and leucine rich repeat containing"""	22937	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"""	609660	"""NACHT, leucine rich repeat and PYD containing 13"""	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.160C>T	19.37:g.56443518G>A	ENSP00000343891:p.Arg54Cys		61135330	Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	37	CCDS33119.1	.	.	.	.	.	.	.	.	.	.	G	1.292	-0.607384	0.03717	.	.	ENSG00000173572	ENST00000342929	T	0.53206	0.63	1.97	-3.94	0.04130	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.28134	0.0694	L	0.32530	0.975	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.12066	-1.0562	9	0.56958	D	0.05	.	0.3437	0.00338	0.3405:0.1354:0.1752:0.3489	.	54	Q86W25	NAL13_HUMAN	C	54	ENSP00000343891:R54C	ENSP00000343891:R54C	R	-	1	0	NLRP13	61135330	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.167000	0.03126	-2.817000	0.00345	-2.097000	0.00363	CGT		0.557	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
NLRP8	126205	hgsc.bcm.edu	37	19	56466193	56466193	+	Missense_Mutation	SNP	T	T	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:56466193T>A	ENST00000291971.3	+	3	840	c.769T>A	c.(769-771)Tcc>Acc	p.S257T	NLRP8_ENST00000590542.1_Missense_Mutation_p.S257T	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	257	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		CCAGAGCTTCTCCGAGCTGAT	0.512																																																	0			19											154.0	151.0	152.0					19																	56466193		2203	4300	6503	61158005	SO:0001583	missense	126205			AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.769T>A	19.37:g.56466193T>A	ENSP00000291971:p.Ser257Thr		61158005	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	.	.	.	.	.	.	.	.	.	.	T	12.73	2.024878	0.35701	.	.	ENSG00000179709	ENST00000291971	T	0.23552	1.9	2.04	0.977	0.19733	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.17916	0.0430	N	0.16368	0.405	0.09310	N	1	D;B	0.53312	0.959;0.242	P;B	0.48552	0.581;0.166	T	0.10847	-1.0612	9	0.44086	T	0.13	.	5.0815	0.14659	0.0:0.0:0.3094:0.6906	.	257;257	Q86W28-2;Q86W28	.;NALP8_HUMAN	T	257	ENSP00000291971:S257T	ENSP00000291971:S257T	S	+	1	0	NLRP8	61158005	0.000000	0.05858	0.003000	0.11579	0.028000	0.11728	0.109000	0.15417	0.219000	0.20840	0.421000	0.28195	TCC		0.512	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
AURKC	6795	hgsc.bcm.edu	37	19	57744834	57744834	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:57744834G>T	ENST00000302804.7	+	5	628	c.442G>T	c.(442-444)Gag>Tag	p.E148*	AURKC_ENST00000599062.1_Nonsense_Mutation_p.E145*|AURKC_ENST00000598785.1_Nonsense_Mutation_p.E114*|AURKC_ENST00000448930.1_Nonsense_Mutation_p.E114*|AURKC_ENST00000415300.2_Nonsense_Mutation_p.E129*	NM_001015878.1	NP_001015878.1	Q9UQB9	AURKC_HUMAN	aurora kinase C	148	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> Q (in a lung squamous cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		attachment of spindle microtubules to kinetochore (GO:0008608)|cytokinesis (GO:0000910)|histone modification (GO:0016570)|meiotic nuclear division (GO:0007126)|positive regulation of cytokinesis (GO:0032467)|protein phosphorylation (GO:0006468)|spindle midzone assembly involved in mitosis (GO:0051256)	chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.E114*(1)|p.E148*(1)|p.E114Q(1)		breast(1)|endometrium(1)|large_intestine(9)|lung(9)|ovary(3)|prostate(1)|stomach(1)	25		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0122)		ACAGATAATAGAGGAGTTGGC	0.478																																																	3	Substitution - Nonsense(2)|Substitution - Missense(1)	lung(3)	19											98.0	96.0	97.0					19																	57744834		2203	4300	6503	62436646	SO:0001587	stop_gained	6795				CCDS33128.1, CCDS46205.1, CCDS46206.1	19q13.43	2013-09-19	2003-07-21	2003-07-23	ENSG00000105146	ENSG00000105146			11391	protein-coding gene	gene with protein product		603495	"""serine/threonine kinase 13 (aurora/IPL1-like)"""	STK13		9799611	Standard	XR_430209		Approved	AurC, ARK3	uc002qoe.3	Q9UQB9	OTTHUMG00000183106	ENST00000302804.7:c.442G>T	19.37:g.57744834G>T	ENSP00000302898:p.Glu148*		62436646	O60681|O75442|Q6AZY8|Q6DLZ0|Q9UPK5	Nonsense_Mutation	SNP	ENST00000302804.7	37	CCDS33128.1	.	.	.	.	.	.	.	.	.	.	G	36	5.829037	0.96996	.	.	ENSG00000105146	ENST00000415300;ENST00000448930;ENST00000302804	.	.	.	3.67	2.61	0.31194	.	0.050269	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-32.584	11.5835	0.50904	0.0:0.1816:0.8184:0.0	.	.	.	.	X	129;114;148	.	ENSP00000302898:E148X	E	+	1	0	AURKC	62436646	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	2.741000	0.47426	1.107000	0.41642	0.462000	0.41574	GAG		0.478	AURKC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465089.1	NM_003160	
NPBWR1	2831	hgsc.bcm.edu	37	8	53852612	53852612	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:53852612G>A	ENST00000331251.3	+	1	1622	c.145G>A	c.(145-147)Gcc>Acc	p.A49T		NM_005285.3	NP_005276.2	P48145	NPBW1_HUMAN	neuropeptides B/W receptor 1	49					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)|regulation of metabolic process (GO:0019222)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)	p.A49T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)	17		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)				GGTGATCTGCGCCGTGGGTCT	0.697																																																	1	Substitution - Missense(1)	large_intestine(1)	8											33.0	30.0	31.0					8																	53852612		2202	4298	6500	54015165	SO:0001583	missense	2831			BC033145	CCDS6151.1	8p22-q21.13	2012-08-08	2006-02-15	2006-02-15		ENSG00000183729		"""GPCR / Class A : Neuropeptide receptors : W/B"""	4522	protein-coding gene	gene with protein product		600730	"""G protein-coupled receptor 7"""	GPR7		7590751, 12401809	Standard	NM_005285		Approved		uc011ldu.2	P48145		ENST00000331251.3:c.145G>A	8.37:g.53852612G>A	ENSP00000330284:p.Ala49Thr		54015165	Q6NTC7	Missense_Mutation	SNP	ENST00000331251.3	37	CCDS6151.1	.	.	.	.	.	.	.	.	.	.	G	36	5.903824	0.97087	.	.	ENSG00000183729	ENST00000331251	T	0.37235	1.21	4.74	4.74	0.60224	.	0.115150	0.36815	N	0.002381	T	0.38558	0.1045	N	0.08118	0	0.58432	D	0.999998	D	0.76494	0.999	P	0.62435	0.902	T	0.49826	-0.8898	10	0.52906	T	0.07	.	17.9109	0.88934	0.0:0.0:1.0:0.0	.	49	P48145	NPBW1_HUMAN	T	49	ENSP00000330284:A49T	ENSP00000330284:A49T	A	+	1	0	NPBWR1	54015165	1.000000	0.71417	0.987000	0.45799	0.935000	0.57460	7.403000	0.79983	2.457000	0.83068	0.655000	0.94253	GCC		0.697	NPBWR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378047.1	NM_005285	
PRDM14	63978	hgsc.bcm.edu	37	8	70964378	70964378	+	Silent	SNP	G	G	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:70964378G>T	ENST00000276594.2	-	8	1851	c.1650C>A	c.(1648-1650)atC>atA	p.I550I		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	550					cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			TTTTCCCACAGATGCTGCATG	0.478																																					NSCLC(129;99 1813 5906 40656 46114)												0			8											120.0	113.0	116.0					8																	70964378		2203	4300	6503	71126932	SO:0001819	synonymous_variant	63978			AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"""Zinc fingers, C2H2-type"""	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.1650C>A	8.37:g.70964378G>T			71126932	Q86UX9	Silent	SNP	ENST00000276594.2	37	CCDS6206.1																																																																																				0.478	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1		
PRDM14	63978	hgsc.bcm.edu	37	8	70978671	70978671	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:70978671C>T	ENST00000276594.2	-	5	1183	c.982G>A	c.(982-984)Gtc>Atc	p.V328I		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	328	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.V328I(1)		NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			GCACAGTTGACATAGGACATC	0.428																																					NSCLC(129;99 1813 5906 40656 46114)												1	Substitution - Missense(1)	ovary(1)	8											128.0	125.0	126.0					8																	70978671		2203	4300	6503	71141225	SO:0001583	missense	63978			AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"""Zinc fingers, C2H2-type"""	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.982G>A	8.37:g.70978671C>T	ENSP00000276594:p.Val328Ile		71141225	Q86UX9	Missense_Mutation	SNP	ENST00000276594.2	37	CCDS6206.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.682484	0.88542	.	.	ENSG00000147596	ENST00000276594	T	0.78595	-1.19	5.89	5.89	0.94794	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.83968	0.5369	L	0.41492	1.28	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78909	-0.2018	10	0.22109	T	0.4	-29.9487	20.2618	0.98447	0.0:1.0:0.0:0.0	.	328	Q9GZV8	PRD14_HUMAN	I	328	ENSP00000276594:V328I	ENSP00000276594:V328I	V	-	1	0	PRDM14	71141225	1.000000	0.71417	0.993000	0.49108	0.971000	0.66376	7.481000	0.81124	2.793000	0.96121	0.655000	0.94253	GTC		0.428	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1		
RUNX1T1	862	hgsc.bcm.edu	37	8	92998451	92998451	+	Missense_Mutation	SNP	G	G	A	rs200248598		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:92998451G>A	ENST00000523629.1	-	9	1634	c.1180C>T	c.(1180-1182)Cgg>Tgg	p.R394W	RUNX1T1_ENST00000518844.1_Missense_Mutation_p.R367W|RUNX1T1_ENST00000520724.1_Missense_Mutation_p.R357W|RUNX1T1_ENST00000360348.2_Missense_Mutation_p.R357W|RUNX1T1_ENST00000265814.3_Missense_Mutation_p.R394W|RUNX1T1_ENST00000422361.2_Missense_Mutation_p.R357W|RUNX1T1_ENST00000436581.2_Missense_Mutation_p.R405W|RUNX1T1_ENST00000396218.1_Missense_Mutation_p.R367W	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	394					fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R357W(1)|p.R405W(1)|p.R394W(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			CTGTACCGCCGGATCCAGTAA	0.517													G|||	1	0.000199681	0.0	0.0	5008	,	,		14722	0.0		0.001	False		,,,				2504	0.0																3	Substitution - Missense(3)	lung(3)	8											119.0	120.0	120.0					8																	92998451		2203	4300	6503	93067627	SO:0001583	missense	862			D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"""Zinc fingers, MYND-type"""	1535	protein-coding gene	gene with protein product		133435	"""core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"""	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.1180C>T	8.37:g.92998451G>A	ENSP00000428543:p.Arg394Trp		93067627	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	37	CCDS6256.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	29.1	4.978612	0.92982	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844	T;T;T;T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2	5.67	5.67	0.87782	NHR2-like (1);	0.000000	0.85682	D	0.000000	T	0.77942	0.4206	M	0.69823	2.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;1.0;0.996	T	0.79711	-0.1689	10	0.87932	D	0	-16.5075	14.5933	0.68386	0.0:0.0:0.8542:0.1458	.	405;394;367	E7EPN4;Q06455;Q06455-2	.;MTG8_HUMAN;.	W	394;367;394;357;357;357;405;367	ENSP00000428543:R394W;ENSP00000379520:R367W;ENSP00000265814:R394W;ENSP00000353504:R357W;ENSP00000390137:R357W;ENSP00000428742:R357W;ENSP00000402257:R405W;ENSP00000430728:R367W	ENSP00000265814:R394W	R	-	1	2	RUNX1T1	93067627	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.515000	0.60489	2.677000	0.91161	0.655000	0.94253	CGG		0.517	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635	
TMEM67	91147	hgsc.bcm.edu	37	8	94809683	94809683	+	Silent	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:94809683C>T	ENST00000453321.3	+	20	2143	c.2085C>T	c.(2083-2085)gtC>gtT	p.V695V	TMEM67_ENST00000409623.3_Silent_p.V614V	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67	695					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)	p.V685V(1)		breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			TACTTACTGTCCTCTTCTTTT	0.299																																																	1	Substitution - coding silent(1)	ovary(1)	8											111.0	106.0	108.0					8																	94809683		2203	4300	6503	94878859	SO:0001819	synonymous_variant	91147			BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"""Meckelin"""	609884	"""Meckel syndrome, type 3"""	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	ENST00000453321.3:c.2085C>T	8.37:g.94809683C>T			94878859	B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Silent	SNP	ENST00000453321.3	37	CCDS6258.2																																																																																				0.299	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704	
CSMD3	114788	hgsc.bcm.edu	37	8	113241027	113241027	+	Missense_Mutation	SNP	G	G	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:113241027G>T	ENST00000297405.5	-	70	11166	c.10922C>A	c.(10921-10923)gCa>gAa	p.A3641E	CSMD3_ENST00000343508.3_Missense_Mutation_p.A3601E|CSMD3_ENST00000455883.2_Missense_Mutation_p.A3472E|CSMD3_ENST00000352409.3_Missense_Mutation_p.A3571E	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3641						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AAATATAAGTGCAAAAAAAGG	0.303										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																							0			8											79.0	82.0	81.0					8																	113241027		2203	4297	6500	113310203	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.10922C>A	8.37:g.113241027G>T	ENSP00000297405:p.Ala3641Glu		113310203	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	33	5.227201	0.95173	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.40476	1.39;1.38;1.45;1.03;1.42	5.68	5.68	0.88126	.	0.000000	0.64402	D	0.000001	T	0.66829	0.2829	M	0.73217	2.22	0.80722	D	1	D;D;P	0.89917	1.0;0.999;0.845	D;D;P	0.87578	0.998;0.995;0.458	T	0.67741	-0.5592	10	0.87932	D	0	.	20.14	0.98056	0.0:0.0:1.0:0.0	.	3472;3641;3601	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	E	3601;3641;2911;3472;3571	ENSP00000345799:A3601E;ENSP00000297405:A3641E;ENSP00000341558:A2911E;ENSP00000412263:A3472E;ENSP00000343124:A3571E	ENSP00000297405:A3641E	A	-	2	0	CSMD3	113310203	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.813000	0.99286	2.837000	0.97791	0.591000	0.81541	GCA		0.303	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
CSMD3	114788	hgsc.bcm.edu	37	8	113275951	113275951	+	Missense_Mutation	SNP	G	G	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:113275951G>T	ENST00000297405.5	-	61	10023	c.9779C>A	c.(9778-9780)tCt>tAt	p.S3260Y	CSMD3_ENST00000343508.3_Missense_Mutation_p.S3220Y|CSMD3_ENST00000455883.2_Missense_Mutation_p.S3091Y|CSMD3_ENST00000352409.3_Missense_Mutation_p.S3190Y	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3260	Sushi 25. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ATAGCCTGGAGAACAGATGTA	0.473										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																							0			8											108.0	91.0	97.0					8																	113275951		2203	4300	6503	113345127	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.9779C>A	8.37:g.113275951G>T	ENSP00000297405:p.Ser3260Tyr		113345127	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	12.60	1.985315	0.35036	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13;-0.13	5.76	5.76	0.90799	Complement control module (2);Sushi/SCR/CCP (3);	0.194332	0.37261	N	0.002175	T	0.69744	0.3145	N	0.25789	0.76	0.80722	D	1	P;D;D	0.71674	0.951;0.961;0.998	P;P;D	0.69479	0.864;0.905;0.964	T	0.67979	-0.5530	10	0.38643	T	0.18	.	19.9759	0.97304	0.0:0.0:1.0:0.0	.	3091;3260;3220	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	Y	3220;3260;2530;3091;3190	ENSP00000345799:S3220Y;ENSP00000297405:S3260Y;ENSP00000341558:S2530Y;ENSP00000412263:S3091Y;ENSP00000343124:S3190Y	ENSP00000297405:S3260Y	S	-	2	0	CSMD3	113345127	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.942000	0.63547	2.713000	0.92767	0.655000	0.94253	TCT		0.473	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
CSMD3	114788	hgsc.bcm.edu	37	8	113392655	113392655	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:113392655G>A	ENST00000297405.5	-	38	6306	c.6062C>T	c.(6061-6063)aCg>aTg	p.T2021M	CSMD3_ENST00000343508.3_Missense_Mutation_p.T1981M|CSMD3_ENST00000455883.2_Missense_Mutation_p.T1917M|CSMD3_ENST00000352409.3_Missense_Mutation_p.T1951M	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2021	CUB 11. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T2021K(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ATTATTAGACGTACTATTCAA	0.303										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																							1	Substitution - Missense(1)	ovary(1)	8											105.0	112.0	110.0					8																	113392655		2203	4292	6495	113461831	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.6062C>T	8.37:g.113392655G>A	ENSP00000297405:p.Thr2021Met		113461831	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.263582	0.80358	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.19806	2.12;2.12;2.12;2.12;2.12	5.64	5.64	0.86602	CUB (5);	0.000000	0.64402	D	0.000001	T	0.56717	0.2004	M	0.90252	3.1	0.52099	D	0.999941	D;P;D	0.89917	1.0;0.955;1.0	D;P;D	0.97110	0.999;0.816;1.0	T	0.62891	-0.6758	10	0.52906	T	0.07	.	19.2842	0.94065	0.0:0.0:1.0:0.0	.	1917;2021;1981	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	M	1981;2021;1291;1917;1951	ENSP00000345799:T1981M;ENSP00000297405:T2021M;ENSP00000341558:T1291M;ENSP00000412263:T1917M;ENSP00000343124:T1951M	ENSP00000297405:T2021M	T	-	2	0	CSMD3	113461831	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.573000	0.82421	2.654000	0.90174	0.591000	0.81541	ACG		0.303	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
ADCY8	114	hgsc.bcm.edu	37	8	132051814	132051814	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr8:132051814G>A	ENST00000286355.5	-	1	2858	c.766C>T	c.(766-768)Cag>Tag	p.Q256*	ADCY8_ENST00000377928.3_Nonsense_Mutation_p.Q256*	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	256					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.Q256*(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			GCCAGGATCTGGGTGGTCATG	0.642										HNSCC(32;0.087)																																							1	Substitution - Nonsense(1)	upper_aerodigestive_tract(1)	8											46.0	41.0	43.0					8																	132051814		2203	4300	6503	132120996	SO:0001587	stop_gained	114			Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"""Adenylate cyclases"""	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.766C>T	8.37:g.132051814G>A	ENSP00000286355:p.Gln256*		132120996		Nonsense_Mutation	SNP	ENST00000286355.5	37	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	G	54	22.537047	0.99949	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	.	.	.	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	.	18.2863	0.90115	0.0:0.0:1.0:0.0	.	.	.	.	X	256	.	ENSP00000286355:Q256X	Q	-	1	0	ADCY8	132120996	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.444000	0.97578	2.580000	0.87095	0.455000	0.32223	CAG		0.642	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1		
ARID1A	8289	hgsc.bcm.edu	37	1	27105551	27105551	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:27105551G>A	ENST00000324856.7	+	20	5533	c.5162G>A	c.(5161-5163)cGa>cAa	p.R1721Q	ARID1A_ENST00000374152.2_Missense_Mutation_p.R1338Q|ARID1A_ENST00000540690.1_Missense_Mutation_p.R49Q|ARID1A_ENST00000457599.2_Missense_Mutation_p.R1504Q	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1721					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GAATATTTCCGACGATGCCTG	0.443			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																			Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	0			1											183.0	201.0	195.0					1																	27105551		2203	4300	6503	26978138	SO:0001583	missense	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5162G>A	1.37:g.27105551G>A	ENSP00000320485:p.Arg1721Gln		26978138	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.138378	0.77775	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152;ENST00000540690	T;T;T;T	0.12774	4.19;4.07;4.02;2.65	4.71	4.71	0.59529	.	0.060827	0.64402	D	0.000007	T	0.37625	0.1010	M	0.71206	2.165	0.49389	D	0.999786	P;P;D	0.76494	0.95;0.917;0.999	P;P;D	0.77557	0.498;0.459;0.99	T	0.05989	-1.0852	10	0.42905	T	0.14	-6.2012	18.208	0.89860	0.0:0.0:1.0:0.0	.	1338;1721;1504	O14497-3;O14497;O14497-2	.;ARI1A_HUMAN;.	Q	1721;1504;1338;49	ENSP00000320485:R1721Q;ENSP00000387636:R1504Q;ENSP00000363267:R1338Q;ENSP00000442437:R49Q	ENSP00000320485:R1721Q	R	+	2	0	ARID1A	26978138	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.084000	0.94076	2.622000	0.88805	0.591000	0.81541	CGA		0.443	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
RBBP4	5928	hgsc.bcm.edu	37	1	33123108	33123108	+	Missense_Mutation	SNP	C	C	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:33123108C>A	ENST00000373493.5	+	3	404	c.245C>A	c.(244-246)gCc>gAc	p.A82D	RBBP4_ENST00000524393.1_Intron|RBBP4_ENST00000373485.1_Missense_Mutation_p.A82D|RBBP4_ENST00000544435.1_Intron|RBBP4_ENST00000458695.2_Missense_Mutation_p.A47D|RBBP4_ENST00000414241.3_Missense_Mutation_p.A81D	NM_001135255.1|NM_005610.2	NP_001128727.1|NP_005601.1	Q09028	RBBP4_HUMAN	retinoblastoma binding protein 4	82					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin assembly (GO:0031497)|chromatin remodeling (GO:0006338)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|nucleosome assembly (GO:0006334)|regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|NURF complex (GO:0016589)|protein complex (GO:0043234)|Sin3 complex (GO:0016580)	histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)	p.A82D(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|prostate(4)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				CTTGTTATAGCCAGTGTGCAG	0.433																																																	1	Substitution - Missense(1)	ovary(1)	1											126.0	105.0	112.0					1																	33123108		2203	4300	6503	32895695	SO:0001583	missense	5928			BC053904	CCDS366.1, CCDS44105.1, CCDS44106.1	1p35.1	2014-07-17	2001-11-28		ENSG00000162521	ENSG00000162521		"""WD repeat domain containing"""	9887	protein-coding gene	gene with protein product		602923	"""retinoblastoma-binding protein 4"""			8350924, 14609955, 17531812	Standard	NM_005610		Approved	RbAp48, NURF55, lin-53	uc001bvr.3	Q09028	OTTHUMG00000007998	ENST00000373493.5:c.245C>A	1.37:g.33123108C>A	ENSP00000362592:p.Ala82Asp		32895695	B2R6G9|B4DRH0|D3DPQ3|P31149|Q53H02|Q96BV9	Missense_Mutation	SNP	ENST00000373493.5	37	CCDS366.1	.	.	.	.	.	.	.	.	.	.	C	33	5.265493	0.95399	.	.	ENSG00000162521	ENST00000414241;ENST00000373493;ENST00000373485;ENST00000458695;ENST00000490500;ENST00000445722	T;T;T;T	0.71934	-0.58;-0.61;-0.5;-0.56	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	D	0.88865	0.6553	H	0.96943	3.91	0.80722	D	1	D;P	0.56035	0.974;0.955	P;P	0.61592	0.644;0.891	D	0.92463	0.5979	10	0.87932	D	0	.	18.1598	0.89705	0.0:1.0:0.0:0.0	.	81;82	Q09028-2;Q09028	.;RBBP4_HUMAN	D	81;82;82;47;47;47	ENSP00000398242:A81D;ENSP00000362592:A82D;ENSP00000362584:A82D;ENSP00000396057:A47D	ENSP00000362584:A82D	A	+	2	0	RBBP4	32895695	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.692000	0.84203	2.607000	0.88179	0.561000	0.74099	GCC		0.433	RBBP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021957.3	NM_005610	
MPL	4352	hgsc.bcm.edu	37	1	43805162	43805162	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:43805162T>C	ENST00000372470.3	+	4	654	c.612T>C	c.(610-612)tcT>tcC	p.S204S	MPL_ENST00000413998.2_Silent_p.S204S	NM_005373.2	NP_005364.1	P40238	TPOR_HUMAN	MPL proto-oncogene, thrombopoietin receptor	204	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|platelet activation (GO:0030168)|regulation of chemokine production (GO:0032642)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(551)|large_intestine(3)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	567	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			Eltrombopag(DB06210)|Romiplostim(DB05332)	ACTCAGCCTCTGCTCTGGACC	0.572			Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia																														NSCLC(52;534 1204 10016 41452 44427)		yes	Dom	yes	Familial essential thrombocythemia	1	p34	4352	"""myeloproliferative leukemia virus oncogene, thrombopoietin receptor"""	yes	L	0			1											86.0	83.0	84.0					1																	43805162		2203	4300	6503	43577749	SO:0001819	synonymous_variant	4352			M90102	CCDS483.1	1p34	2014-09-17	2014-06-26		ENSG00000117400	ENSG00000117400		"""CD molecules"", ""Fibronectin type III domain containing"""	7217	protein-coding gene	gene with protein product		159530	"""myeloproliferative leukemia virus oncogene"""			1608974	Standard	NM_005373		Approved	CD110, TPOR	uc001ciw.3	P40238	OTTHUMG00000007429	ENST00000372470.3:c.612T>C	1.37:g.43805162T>C			43577749	Q5JUZ0	Silent	SNP	ENST00000372470.3	37	CCDS483.1																																																																																				0.572	MPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019522.1	NM_005373	
C1orf168	199920	hgsc.bcm.edu	37	1	57189325	57189325	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:57189325T>C	ENST00000343433.6	-	17	1990	c.1910A>G	c.(1909-1911)aAg>aGg	p.K637R	C1orf168_ENST00000484327.1_5'Flank	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	637										NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						GTTTTGCTTCTTGGTTTTGAA	0.313																																																	0			1											54.0	52.0	52.0					1																	57189325		2201	4296	6497	56961913	SO:0001583	missense	199920			BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.1910A>G	1.37:g.57189325T>C	ENSP00000345972:p.Lys637Arg		56961913	Q63HM3|Q6ZUY6	Missense_Mutation	SNP	ENST00000343433.6	37	CCDS30729.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.155752	0.78114	.	.	ENSG00000187889	ENST00000343433	T	0.37584	1.19	4.74	4.74	0.60224	.	0.000000	0.53938	D	0.000049	T	0.54565	0.1866	M	0.68317	2.08	0.33587	D	0.600617	D	0.76494	0.999	D	0.66351	0.943	T	0.68907	-0.5285	10	0.66056	D	0.02	-11.5604	12.1494	0.54042	0.0:0.0:0.0:1.0	.	637	Q5VWT5	CA168_HUMAN	R	637	ENSP00000345972:K637R	ENSP00000345972:K637R	K	-	2	0	C1orf168	56961913	1.000000	0.71417	0.992000	0.48379	0.924000	0.55760	1.813000	0.38962	2.119000	0.64992	0.533000	0.62120	AAG		0.313	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303	
ST6GALNAC3	256435	hgsc.bcm.edu	37	1	76877830	76877830	+	Silent	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:76877830A>G	ENST00000328299.3	+	3	499	c.351A>G	c.(349-351)gaA>gaG	p.E117E	ST6GALNAC3_ENST00000464140.1_3'UTR	NM_152996.2	NP_694541.2	Q8NDV1	SIA7C_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	117					glycoprotein metabolic process (GO:0009100)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide metabolic process (GO:0006677)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sialyltransferase activity (GO:0008373)	p.E117E(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|ovary(3)|prostate(1)|skin(2)	36						GTTATGAAGAAGATGTCGGCC	0.448																																																	1	Substitution - coding silent(1)	ovary(1)	1											128.0	116.0	120.0					1																	76877830		2203	4300	6503	76650418	SO:0001819	synonymous_variant	256435				CCDS672.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000184005	ENSG00000184005		"""Sialyltransferases"""	19343	protein-coding gene	gene with protein product	"""ST6GALNAC III"""	610133	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) C"""	SIAT7C			Standard	NM_152996		Approved		uc001dhh.2	Q8NDV1	OTTHUMG00000009615	ENST00000328299.3:c.351A>G	1.37:g.76877830A>G			76650418	Q6PCE0|Q6UX29|Q8N259	Silent	SNP	ENST00000328299.3	37	CCDS672.1																																																																																				0.448	ST6GALNAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026501.1	NM_152996	
CHIA	27159	hgsc.bcm.edu	37	1	111861256	111861256	+	Missense_Mutation	SNP	G	G	T	rs549528699		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:111861256G>T	ENST00000369740.1	+	9	974	c.871G>T	c.(871-873)Gct>Tct	p.A291S	CHIA_ENST00000343320.6_Missense_Mutation_p.A291S|CHIA_ENST00000451398.2_Missense_Mutation_p.A130S|RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000483391.1_Missense_Mutation_p.A130S|CHIA_ENST00000430615.1_Missense_Mutation_p.A183S|CHIA_ENST00000353665.6_Missense_Mutation_p.A130S	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	291					apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		TGCTGGTCCTGCTGGGCCCTA	0.537													G|||	1	0.000199681	0.0	0.0	5008	,	,		19581	0.0		0.0	False		,,,				2504	0.001																0			1											144.0	139.0	141.0					1																	111861256		2203	4300	6503	111662779	SO:0001583	missense	27159			AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.871G>T	1.37:g.111861256G>T	ENSP00000358755:p.Ala291Ser		111662779	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	37	CCDS41368.1	.	.	.	.	.	.	.	.	.	.	G	17.75	3.466533	0.63625	.	.	ENSG00000134216	ENST00000422815;ENST00000483391;ENST00000369740;ENST00000343320;ENST00000451398;ENST00000353665;ENST00000489524;ENST00000430615	T;T;T;T;T;T;T;T	0.05855	3.38;3.38;3.38;3.38;3.38;3.38;3.38;3.38	4.84	1.57	0.23409	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.176583	0.34507	N	0.003915	T	0.09598	0.0236	L	0.51914	1.62	0.45822	D	0.998694	P	0.35011	0.48	P	0.57911	0.829	T	0.05386	-1.0888	10	0.37606	T	0.19	-6.1937	13.709	0.62656	0.0:0.4607:0.5393:0.0	.	291	Q9BZP6	CHIA_HUMAN	S	235;130;291;291;130;130;130;183	ENSP00000387671:A235S;ENSP00000436946:A130S;ENSP00000358755:A291S;ENSP00000341828:A291S;ENSP00000390476:A130S;ENSP00000338970:A130S;ENSP00000433309:A130S;ENSP00000391132:A183S	ENSP00000341828:A291S	A	+	1	0	CHIA	111662779	0.993000	0.37304	0.998000	0.56505	0.910000	0.53928	2.085000	0.41634	0.521000	0.28445	0.563000	0.77884	GCT		0.537	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
KCND3	3752	hgsc.bcm.edu	37	1	112329627	112329627	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:112329627A>G	ENST00000315987.2	-	3	1687	c.1208T>C	c.(1207-1209)gTt>gCt	p.V403A	KCND3_ENST00000302127.4_Missense_Mutation_p.V403A|KCND3_ENST00000369697.1_Missense_Mutation_p.V403A	NM_004980.4	NP_004971.2	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 3	403					cell death (GO:0008219)|membrane repolarization (GO:0086009)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	49		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)	Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	AAAGTTGGAAACAATCACAGG	0.537																																																	0			1											126.0	116.0	120.0					1																	112329627		2203	4300	6503	112131150	SO:0001583	missense	3752			AF048713	CCDS843.1, CCDS844.1	1p13.2	2014-09-17			ENSG00000171385	ENSG00000171385		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6239	protein-coding gene	gene with protein product		605411	"""spinocerebellar ataxia 22"", ""spinocerebellar ataxia 19"""	SCA22, SCA19		10942109, 16382104, 23280837	Standard	NM_172198		Approved	Kv4.3, KSHIVB	uc001ebu.1	Q9UK17	OTTHUMG00000011989	ENST00000315987.2:c.1208T>C	1.37:g.112329627A>G	ENSP00000319591:p.Val403Ala		112131150	O60576|O60577|Q14D71|Q5T0M0|Q9UH85|Q9UH86|Q9UK16	Missense_Mutation	SNP	ENST00000315987.2	37	CCDS843.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.808423	0.90707	.	.	ENSG00000171385	ENST00000369697;ENST00000315987;ENST00000302127	D;D;D	0.97279	-4.32;-4.32;-4.32	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	D	0.97961	0.9329	M	0.79123	2.44	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.991	D	0.99180	1.0867	10	0.87932	D	0	.	14.3685	0.66823	1.0:0.0:0.0:0.0	.	403;403	Q14D71;Q9UK17	.;KCND3_HUMAN	A	403	ENSP00000358711:V403A;ENSP00000319591:V403A;ENSP00000306923:V403A	ENSP00000306923:V403A	V	-	2	0	KCND3	112131150	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.339000	0.96797	1.942000	0.56320	0.459000	0.35465	GTT		0.537	KCND3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000033144.1	NM_172198	
LCE1D	353134	hgsc.bcm.edu	37	1	152770576	152770576	+	Silent	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:152770576C>T	ENST00000326233.6	+	2	349	c.306C>T	c.(304-306)tgC>tgT	p.C102C		NM_178352.2	NP_848129.1	Q5T752	LCE1D_HUMAN	late cornified envelope 1D	102	Cys-rich.				cellular response to calcium ion (GO:0071277)|cognition (GO:0050890)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(1)	1	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCAGCTGCTGCGGTGGGGGCA	0.637																																																	0			1											44.0	40.0	41.0					1																	152770576		2018	3691	5709	151037200	SO:0001819	synonymous_variant	353134				CCDS1025.1	1q21.3	2008-02-05			ENSG00000172155	ENSG00000172155		"""Late cornified envelopes"""	29465	protein-coding gene	gene with protein product		612606				11698679	Standard	NM_178352		Approved	LEP4	uc009wnp.3	Q5T752	OTTHUMG00000012444	ENST00000326233.6:c.306C>T	1.37:g.152770576C>T			151037200		Silent	SNP	ENST00000326233.6	37	CCDS1025.1																																																																																				0.637	LCE1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034657.2	NM_178352	
PKLR	5313	hgsc.bcm.edu	37	1	155264373	155264373	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:155264373G>A	ENST00000342741.4	-	6	903	c.865C>T	c.(865-867)Cgg>Tgg	p.R289W	PKLR_ENST00000392414.3_Missense_Mutation_p.R258W	NM_000298.5	NP_000289.1	P30613	KPYR_HUMAN	pyruvate kinase, liver and RBC	289					ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of cellular metabolic process (GO:0031325)|pyruvate biosynthetic process (GO:0042866)|response to ATP (GO:0033198)|response to cAMP (GO:0051591)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to nutrient (GO:0007584)|response to other organism (GO:0051707)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(78;6.99e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;3.18e-10)|all cancers(21;7.9e-10)|BRCA - Breast invasive adenocarcinoma(34;0.00116)|LUSC - Lung squamous cell carcinoma(543;0.127)		Pyruvic acid(DB00119)	CTGGCTTTCCGCACAAAGGAG	0.622																																																	0			1											89.0	79.0	82.0					1																	155264373		2203	4300	6503	153530997	SO:0001583	missense	5313			BC025737, M15465	CCDS1109.1, CCDS44240.1	1q22	2012-10-02			ENSG00000143627	ENSG00000143627	2.7.1.40		9020	protein-coding gene	gene with protein product		609712				3566732	Standard	NM_000298		Approved		uc001fkb.4	P30613	OTTHUMG00000035875	ENST00000342741.4:c.865C>T	1.37:g.155264373G>A	ENSP00000339933:p.Arg289Trp		153530997	O75758|P11973	Missense_Mutation	SNP	ENST00000342741.4	37	CCDS1109.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.390328	0.82902	.	.	ENSG00000143627	ENST00000423816;ENST00000392414;ENST00000342741;ENST00000271946	D;D	0.99793	-6.77;-6.77	4.48	3.55	0.40652	Pyruvate/Phosphoenolpyruvate kinase (2);Pyruvate kinase, barrel (1);	0.000000	0.85682	D	0.000000	D	0.99885	0.9945	H	0.99545	4.62	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.96676	0.9500	10	0.87932	D	0	-24.4399	11.7498	0.51841	0.0:0.0:0.8221:0.1779	.	289;280	P30613;B1AVT1	KPYR_HUMAN;.	W	314;258;289;203	ENSP00000376214:R258W;ENSP00000339933:R289W	ENSP00000271946:R203W	R	-	1	2	PKLR	153530997	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	5.185000	0.65076	1.210000	0.43336	0.467000	0.42956	CGG		0.622	PKLR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087407.2	NM_000298	
ASH1L	55870	hgsc.bcm.edu	37	1	155408817	155408817	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:155408817C>T	ENST00000368346.3	-	5	5768	c.5129G>A	c.(5128-5130)gGg>gAg	p.G1710E	ASH1L_ENST00000392403.3_Missense_Mutation_p.G1710E			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	1710	Ser-rich.				cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			AGAGTCATCCCCAGAAGCAAC	0.433																																																	0			1											53.0	54.0	53.0					1																	155408817		2203	4300	6503	153675441	SO:0001583	missense	55870			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.5129G>A	1.37:g.155408817C>T	ENSP00000357330:p.Gly1710Glu		153675441	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	C	11.72	1.723576	0.30593	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.87729	-2.29;-2.29	5.2	3.13	0.36017	.	1.032010	0.07649	N	0.931665	T	0.60287	0.2257	N	0.08118	0	0.26863	N	0.967914	B;B	0.16603	0.01;0.018	B;B	0.23150	0.02;0.044	T	0.56517	-0.7966	10	0.59425	D	0.04	.	8.6753	0.34176	0.4993:0.408:0.0927:0.0	.	1710;1710	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	E	1710	ENSP00000357330:G1710E;ENSP00000376204:G1710E	ENSP00000357330:G1710E	G	-	2	0	ASH1L	153675441	0.986000	0.35501	0.666000	0.29783	0.983000	0.72400	1.864000	0.39469	0.613000	0.30089	0.563000	0.77884	GGG		0.433	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489	
RGS4	5999	hgsc.bcm.edu	37	1	163044228	163044228	+	Missense_Mutation	SNP	C	C	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:163044228C>A	ENST00000367909.6	+	5	836	c.496C>A	c.(496-498)Cgc>Agc	p.R166S	RGS4_ENST00000421743.2_Missense_Mutation_p.R263S|RGS4_ENST00000527809.1_Missense_Mutation_p.R148S|RGS4_ENST00000367906.3_Missense_Mutation_p.R148S|RGS4_ENST00000491263.1_3'UTR|RGS4_ENST00000367908.4_3'UTR|RGS4_ENST00000531057.1_Intron	NM_001113380.1|NM_005613.5	NP_001106851.1|NP_005604.1	P49798	RGS4_HUMAN	regulator of G-protein signaling 4	166	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				inactivation of MAPK activity (GO:0000188)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)	p.R166C(1)|p.R263S(1)|p.R166S(1)		breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|upper_aerodigestive_tract(2)	21						GGATTCCTACCGCCGCTTCCT	0.502																																					Ovarian(76;1257 1738 3039 6086)												3	Substitution - Missense(3)	lung(2)|ovary(1)	1											233.0	249.0	243.0					1																	163044228		2203	4300	6503	161310852	SO:0001583	missense	5999			BC051869	CCDS1243.1, CCDS44270.1, CCDS44271.1, CCDS44272.1	1q23.3	2008-05-14	2007-08-14		ENSG00000117152	ENSG00000117152		"""Regulators of G-protein signaling"""	10000	protein-coding gene	gene with protein product		602516	"""regulator of G-protein signalling 4"", ""schizophrenia disorder 9"""	SCZD9		8602223, 8756726	Standard	NM_001102445		Approved		uc001gcl.4	P49798	OTTHUMG00000034417	ENST00000367909.6:c.496C>A	1.37:g.163044228C>A	ENSP00000356885:p.Arg166Ser		161310852	A7XA56|A7XA58|A7XA59|A7YVV7|B1APZ3	Missense_Mutation	SNP	ENST00000367909.6	37	CCDS1243.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.729493	0.89390	.	.	ENSG00000117152	ENST00000421743;ENST00000367909;ENST00000527809;ENST00000367906	T;T;T;T	0.01854	4.6;4.6;4.6;4.6	4.84	4.84	0.62591	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.058915	0.64402	D	0.000002	T	0.02649	0.0080	N	0.17800	0.525	0.47905	D	0.999542	P;D	0.64830	0.929;0.994	P;P	0.61275	0.746;0.886	T	0.58589	-0.7610	9	0.66056	D	0.02	.	15.4794	0.75514	0.0:1.0:0.0:0.0	.	166;263	P49798;A7XA59	RGS4_HUMAN;.	S	263;166;148;148	ENSP00000397181:R263S;ENSP00000356885:R166S;ENSP00000433261:R148S;ENSP00000356882:R148S	ENSP00000356882:R148S	R	+	1	0	RGS4	161310852	0.990000	0.36364	0.998000	0.56505	0.991000	0.79684	4.564000	0.60830	2.501000	0.84356	0.591000	0.81541	CGC		0.502	RGS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083197.2	NM_005613	
XCL2	6846	hgsc.bcm.edu	37	1	168511319	168511319	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:168511319T>C	ENST00000367819.2	-	2	120	c.88A>G	c.(88-90)Agg>Ggg	p.R30G		NM_003175.3	NP_003166.1	Q9UBD3	XCL2_HUMAN	chemokine (C motif) ligand 2	30					blood circulation (GO:0008015)|cell chemotaxis (GO:0060326)|immune response (GO:0006955)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			large_intestine(1)|lung(6)|ovary(1)	8	all_hematologic(923;0.215)					ACACAGGTCCTCCTATGTGAG	0.453																																																	0			1											119.0	93.0	102.0					1																	168511319		2197	4275	6472	166777943	SO:0001583	missense	6846			BC070309	CCDS1273.1	1q24.2	2013-02-28	2002-08-22	2002-08-23	ENSG00000143185	ENSG00000143185		"""Endogenous ligands"""	10646	protein-coding gene	gene with protein product		604828	"""small inducible cytokine subfamily C, member 2"""	SCYC2		7875320	Standard	NM_003175		Approved	SCM-1b	uc001gfn.4	Q9UBD3	OTTHUMG00000034549	ENST00000367819.2:c.88A>G	1.37:g.168511319T>C	ENSP00000356793:p.Arg30Gly		166777943		Missense_Mutation	SNP	ENST00000367819.2	37	CCDS1273.1	.	.	.	.	.	.	.	.	.	.	T	9.123	1.009467	0.19277	.	.	ENSG00000143185	ENST00000367819	T	0.04406	3.63	2.49	2.49	0.30216	Chemokine interleukin-8-like domain (2);	0.673392	0.14425	N	0.320416	T	0.01061	0.0035	N	0.16478	0.41	0.20703	N	0.999865	B	0.19073	0.033	B	0.22880	0.042	T	0.47315	-0.9127	9	0.28530	T	0.3	-4.923	6.7626	0.23548	0.0:0.0:0.0:1.0	.	30	Q9UBD3	XCL2_HUMAN	G	30	ENSP00000356793:R30G	ENSP00000356793:R30G	R	-	1	2	XCL2	166777943	0.002000	0.14202	0.008000	0.14137	0.039000	0.13416	1.131000	0.31406	1.135000	0.42183	0.164000	0.16699	AGG		0.453	XCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083613.1	NM_003175	
PRRC2C	23215	hgsc.bcm.edu	37	1	171511137	171511137	+	Missense_Mutation	SNP	G	G	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:171511137G>T	ENST00000338920.4	+	16	4763	c.4526G>T	c.(4525-4527)cGa>cTa	p.R1509L	PRRC2C_ENST00000392078.3_Missense_Mutation_p.R1511L|PRRC2C_ENST00000426496.2_Missense_Mutation_p.R1509L|PRRC2C_ENST00000367742.3_Missense_Mutation_p.R1511L	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1509					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										AATGAGAGGCGAGAGAGGGAT	0.398																																																	0			1											66.0	70.0	69.0					1																	171511137		2203	4300	6503	169777761	SO:0001583	missense	0			AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.4526G>T	1.37:g.171511137G>T	ENSP00000343629:p.Arg1509Leu		169777761	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.41|13.41	2.228966|2.228966	0.39399|0.39399	.|.	.|.	ENSG00000117523|ENSG00000117523	ENST00000495585|ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	.|T;T;T;T	.|0.05925	.|3.39;3.37;3.37;3.37	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	.|0.000000	.|0.42294	.|D	.|0.000738	.|T	.|0.21718	.|0.0523	M|M	0.79123|0.79123	2.44|2.44	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	.|T	.|0.00928	.|-1.1511	.|10	.|0.87932	.|D	.|0	.|.	19.7924|19.7924	0.96464|0.96464	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1509	.|Q9Y520-4	.|.	X|L	57|1511;1510;1509;1511;1509;1266	.|ENSP00000375928:R1511L;ENSP00000410219:R1509L;ENSP00000356716:R1511L;ENSP00000343629:R1509L	.|ENSP00000343629:R1509L	E|R	+|+	1|2	0|0	PRRC2C|PRRC2C	169777761|169777761	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.997000|0.997000	0.91878|0.91878	9.461000|9.461000	0.97646|0.97646	2.660000|2.660000	0.90430|0.90430	0.650000|0.650000	0.86243|0.86243	GAG|CGA		0.398	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
ASTN1	460	hgsc.bcm.edu	37	1	176926878	176926878	+	Missense_Mutation	SNP	T	T	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:176926878T>A	ENST00000367654.3	-	11	2058	c.1847A>T	c.(1846-1848)aAc>aTc	p.N616I	ASTN1_ENST00000424564.2_Missense_Mutation_p.N608I|ASTN1_ENST00000361833.2_Missense_Mutation_p.N608I|ASTN1_ENST00000367657.3_Missense_Mutation_p.N608I|ASTN1_ENST00000281881.3_5'UTR	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	616	EGF-like 2.				locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						GCAGCCCCCGTTATCTTTGCT	0.527																																																	0			1											73.0	70.0	71.0					1																	176926878		2203	4300	6503	175193501	SO:0001583	missense	460			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"""astrotactin"""	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.1847A>T	1.37:g.176926878T>A	ENSP00000356626:p.Asn616Ile		175193501	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	37		.	.	.	.	.	.	.	.	.	.	T	27.7	4.851243	0.91355	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.20463	2.07;2.48;2.48;2.07	5.58	5.58	0.84498	Epidermal growth factor-like (1);	0.041188	0.85682	D	0.000000	T	0.35770	0.0943	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;0.997;0.997	D;D;D	0.85130	0.997;0.994;0.994	T	0.15235	-1.0444	10	0.87932	D	0	-36.9469	15.4147	0.74956	0.0:0.0:0.0:1.0	.	616;608;608	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	I	608;608;616;608;608	ENSP00000356629:N608I;ENSP00000354536:N608I;ENSP00000356626:N616I;ENSP00000395041:N608I	ENSP00000354536:N608I	N	-	2	0	ASTN1	175193501	1.000000	0.71417	0.777000	0.31699	0.985000	0.73830	7.555000	0.82223	2.117000	0.64856	0.460000	0.39030	AAC		0.527	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319	
HMCN1	83872	hgsc.bcm.edu	37	1	186106681	186106681	+	Missense_Mutation	SNP	G	G	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:186106681G>C	ENST00000271588.4	+	88	13863	c.13634G>C	c.(13633-13635)tGt>tCt	p.C4545S	HMCN1_ENST00000367492.2_Missense_Mutation_p.C4545S	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4545	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AGTGTCACCTGTGGAAAAGGC	0.463																																																	0			1											70.0	69.0	70.0					1																	186106681		2203	4300	6503	184373304	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.13634G>C	1.37:g.186106681G>C	ENSP00000271588:p.Cys4545Ser		184373304	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	30	5.051235	0.93740	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	D;D	0.96459	-4.02;-4.02	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.98963	0.9647	H	0.98664	4.295	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99282	1.0896	10	0.22706	T	0.39	.	20.0204	0.97499	0.0:0.0:1.0:0.0	.	4545	Q96RW7	HMCN1_HUMAN	S	4545	ENSP00000271588:C4545S;ENSP00000356462:C4545S	ENSP00000271588:C4545S	C	+	2	0	HMCN1	184373304	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.414000	0.97362	2.729000	0.93468	0.650000	0.86243	TGT		0.463	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
KDM5B	10765	hgsc.bcm.edu	37	1	202699086	202699086	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:202699086T>C	ENST00000367265.3	-	26	5410	c.4246A>G	c.(4246-4248)Aga>Gga	p.R1416G	KDM5B_ENST00000367264.2_Missense_Mutation_p.R1452G	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	1416					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						AGGCCCTCTCTTTCCAGGCGT	0.468																																																	0			1											102.0	97.0	99.0					1																	202699086		2203	4300	6503	200965709	SO:0001583	missense	10765			AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	18039	protein-coding gene	gene with protein product	"""cancer/testis antigen 31"", ""protein phosphatase 1, regulatory subunit 98"""	605393	"""Jumonji, AT rich interactive domain 1B (RBP2-like)"", ""jumonji, AT rich interactive domain 1B"""	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.4246A>G	1.37:g.202699086T>C	ENSP00000356234:p.Arg1416Gly		200965709	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	37	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	T	15.95	2.984736	0.53934	.	.	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790	D;D;D	0.86865	-2.18;-1.99;-2.17	5.34	5.34	0.76211	.	0.113338	0.64402	D	0.000013	D	0.90031	0.6887	M	0.63843	1.955	0.44345	D	0.997238	D;D	0.63880	0.993;0.979	D;P	0.63033	0.91;0.628	D	0.88218	0.2895	10	0.30078	T	0.28	-16.9285	9.7879	0.40688	0.0:0.0769:0.0:0.9231	.	1452;1416	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	G	1416;1258;1452;1258	ENSP00000356234:R1416G;ENSP00000356233:R1452G;ENSP00000235790:R1258G	ENSP00000235790:R1258G	R	-	1	2	KDM5B	200965709	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.182000	0.58310	2.013000	0.59113	0.528000	0.53228	AGA		0.468	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618	
RAB29	8934	hgsc.bcm.edu	37	1	205740629	205740629	+	Missense_Mutation	SNP	G	G	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:205740629G>T	ENST00000367139.3	-	4	652	c.349C>A	c.(349-351)Ccg>Acg	p.P117T	RAB7L1_ENST00000235932.4_Missense_Mutation_p.P117T|RAB7L1_ENST00000437324.2_Missense_Mutation_p.P45T|RAB7L1_ENST00000414729.1_Missense_Mutation_p.P117T|RAB7L1_ENST00000446390.2_Missense_Mutation_p.P93T|RAB7L1_ENST00000468887.1_Intron	NM_003929.2	NP_003920.1	O14966	RAB7L_HUMAN		117					cell differentiation (GO:0030154)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|positive regulation of intracellular protein transport (GO:0090316)|protein transport (GO:0015031)|retrograde transport, plasma membrane to Golgi (GO:0035526)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(1)	10	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0194)			CAGGGCACCGGCTCTCCATTG	0.493																																					Pancreas(25;658 872 27763 34889 38531)												0			1											269.0	259.0	262.0					1																	205740629		2203	4300	6503	204007252	SO:0001583	missense	8934																														ENST00000367139.3:c.349C>A	1.37:g.205740629G>T	ENSP00000356107:p.Pro117Thr		204007252	B4E1K3|C9JE77	Missense_Mutation	SNP	ENST00000367139.3	37	CCDS1459.1	.	.	.	.	.	.	.	.	.	.	G	15.60	2.881427	0.51801	.	.	ENSG00000117280	ENST00000367139;ENST00000235932;ENST00000437324;ENST00000446390;ENST00000414729	T;T;T;T;T	0.79352	-1.26;-1.26;-0.4;-1.26;-1.26	5.41	5.41	0.78517	Small GTP-binding protein domain (1);	0.192953	0.45867	D	0.000331	T	0.75503	0.3858	L	0.29908	0.895	0.28008	N	0.935021	D;P	0.54772	0.968;0.566	P;B	0.50314	0.637;0.378	T	0.70945	-0.4734	10	0.40728	T	0.16	-9.7494	16.9603	0.86271	0.0:0.0:1.0:0.0	.	93;117	B4E1K3;O14966	.;RAB7L_HUMAN	T	117;117;45;93;117	ENSP00000356107:P117T;ENSP00000235932:P117T;ENSP00000416613:P45T;ENSP00000389899:P93T;ENSP00000402910:P117T	ENSP00000235932:P117T	P	-	1	0	RAB7L1	204007252	1.000000	0.71417	0.573000	0.28510	0.908000	0.53690	4.869000	0.63028	2.517000	0.84864	0.460000	0.39030	CCG		0.493	RAB7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087732.1		
IL19	29949	hgsc.bcm.edu	37	1	207014388	207014388	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:207014388A>G	ENST00000270218.6	+	6	1342	c.403A>G	c.(403-405)Aat>Gat	p.N135D	IL19_ENST00000340758.2_Missense_Mutation_p.N173D	NM_013371.3	NP_037503.2	Q9UHD0	IL19_HUMAN	interleukin 19	135					apoptotic process (GO:0006915)|immune response (GO:0006955)|interleukin-6 biosynthetic process (GO:0042226)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|reactive oxygen species metabolic process (GO:0072593)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)			central_nervous_system(2)|large_intestine(1)|lung(2)|ovary(1)|stomach(1)	7			BRCA - Breast invasive adenocarcinoma(75;0.211)			GGAAGCCACCAATGCCACCAG	0.522																																																	0			1											126.0	95.0	105.0					1																	207014388		2203	4300	6503	205081011	SO:0001583	missense	29949			AF192498	CCDS1468.1, CCDS1469.1	1q32.2	2008-07-18			ENSG00000142224	ENSG00000142224		"""Interleukins and interleukin receptors"""	5990	protein-coding gene	gene with protein product	"""melanoma differentiation associated protein-like protein"""	605687				11196675	Standard	NM_153758		Approved	IL-19, MDA1, ZMDA1, IL-10C, NG.1	uc001heo.3	Q9UHD0	OTTHUMG00000036387	ENST00000270218.6:c.403A>G	1.37:g.207014388A>G	ENSP00000270218:p.Asn135Asp		205081011	B6VEV9|Q5VUT3|Q96QR4|Q9NUA0	Missense_Mutation	SNP	ENST00000270218.6	37	CCDS1469.1	.	.	.	.	.	.	.	.	.	.	A	8.518	0.868077	0.17250	.	.	ENSG00000142224	ENST00000340758;ENST00000270218	T;T	0.17370	2.28;2.28	5.71	3.19	0.36642	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.561477	0.21175	N	0.078911	T	0.21631	0.0521	M	0.63428	1.95	0.30750	N	0.745213	B;P	0.42296	0.444;0.775	B;P	0.47744	0.255;0.556	T	0.04413	-1.0953	10	0.37606	T	0.19	.	5.5965	0.17329	0.7374:0.173:0.0897:0.0	.	135;173	Q9UHD0;Q5VUT3	IL19_HUMAN;.	D	173;135	ENSP00000343000:N173D;ENSP00000270218:N135D	ENSP00000270218:N135D	N	+	1	0	IL19	205081011	0.078000	0.21339	0.971000	0.41717	0.311000	0.27955	0.448000	0.21726	2.182000	0.69389	0.482000	0.46254	AAT		0.522	IL19-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088567.2	NM_153758	
USH2A	7399	hgsc.bcm.edu	37	1	216591941	216591941	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:216591941C>T	ENST00000307340.3	-	3	952	c.566G>A	c.(565-567)cGc>cAc	p.R189H	USH2A_ENST00000366942.3_Missense_Mutation_p.R189H|USH2A_ENST00000366943.2_Missense_Mutation_p.R189H	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	189					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ATTTACTGTGCGATAATAAAA	0.363										HNSCC(13;0.011)																																							0			1											129.0	123.0	125.0					1																	216591941		2203	4300	6503	214658564	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.566G>A	1.37:g.216591941C>T	ENSP00000305941:p.Arg189His		214658564	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.120714	0.77436	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.74315	-0.83;-0.83;-0.83	5.62	3.76	0.43208	Concanavalin A-like lectin/glucanase (1);LamG-like jellyroll fold (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.43579	U	0.000557	D	0.83147	0.5191	M	0.65975	2.015	0.37858	D	0.929605	D;P	0.89917	1.0;0.798	D;B	0.73380	0.98;0.229	D	0.85453	0.1162	10	0.87932	D	0	.	11.9499	0.52948	0.0:0.8597:0.0:0.1403	.	189;189	O75445-2;O75445	.;USH2A_HUMAN	H	189	ENSP00000305941:R189H;ENSP00000355910:R189H;ENSP00000355909:R189H	ENSP00000305941:R189H	R	-	2	0	USH2A	214658564	1.000000	0.71417	0.993000	0.49108	0.993000	0.82548	1.593000	0.36686	0.729000	0.32403	0.655000	0.94253	CGC		0.363	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
OBSCN	84033	hgsc.bcm.edu	37	1	228475488	228475488	+	Missense_Mutation	SNP	C	C	T	rs375877740		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:228475488C>T	ENST00000422127.1	+	36	9682	c.9638C>T	c.(9637-9639)gCg>gTg	p.A3213V	OBSCN_ENST00000359599.6_Missense_Mutation_p.A2060V|OBSCN_ENST00000366707.4_Missense_Mutation_p.A332V|OBSCN_ENST00000570156.2_Missense_Mutation_p.A3642V|OBSCN_ENST00000366709.4_Missense_Mutation_p.A332V|OBSCN_ENST00000284548.11_Missense_Mutation_p.A3213V	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3213	Ig-like 32.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TCTGTGGCTGCGCCCGTGAAG	0.632																																																	0			1						C	VAL/ALA,VAL/ALA	0,4368		0,0,2184	73.0	83.0	80.0		9638,9638	3.2	0.0	1		80	1,8565		0,1,4282	no	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	64,64	0,1,6466	TT,TC,CC		0.0117,0.0,0.0077	possibly-damaging,possibly-damaging	3213/7969,3213/6621	228475488	1,12933	2184	4283	6467	226542111	SO:0001583	missense	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.9638C>T	1.37:g.228475488C>T	ENSP00000409493:p.Ala3213Val		226542111	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.677575	0.47886	0.0	1.17E-4	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.69806	-0.43;-0.43;-0.43;3.56;-0.43	5.06	3.16	0.36331	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.345259	0.26227	N	0.025598	T	0.74374	0.3708	M	0.65320	2	0.09310	N	1	P;D	0.89917	0.814;1.0	P;D	0.73380	0.49;0.98	T	0.63857	-0.6542	10	0.17369	T	0.5	.	10.2947	0.43616	0.0:0.7901:0.136:0.074	.	3213;3213	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	V	3213;3213;332;332;2060	ENSP00000284548:A3213V;ENSP00000409493:A3213V;ENSP00000355668:A332V;ENSP00000355670:A332V;ENSP00000352613:A2060V	ENSP00000284548:A3213V	A	+	2	0	OBSCN	226542111	0.023000	0.18921	0.001000	0.08648	0.030000	0.12068	0.791000	0.26915	0.522000	0.28464	0.561000	0.74099	GCG		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
GALNT2	2590	hgsc.bcm.edu	37	1	230372430	230372430	+	Missense_Mutation	SNP	A	A	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:230372430A>C	ENST00000366672.4	+	6	638	c.566A>C	c.(565-567)aAa>aCa	p.K189T	GALNT2_ENST00000541865.1_Missense_Mutation_p.K99T|GALNT2_ENST00000543760.1_Missense_Mutation_p.K151T	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	189	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				CTCTTGGGGAAAATTGAGAAA	0.408																																																	0			1											101.0	102.0	102.0					1																	230372430		2203	4300	6503	228439053	SO:0001583	missense	2590			BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4124	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 2"""	602274	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"""			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.566A>C	1.37:g.230372430A>C	ENSP00000355632:p.Lys189Thr		228439053	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Missense_Mutation	SNP	ENST00000366672.4	37	CCDS1582.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.053716	0.55218	.	.	ENSG00000143641	ENST00000543760;ENST00000366672;ENST00000543291;ENST00000541865	T;T;T	0.60548	0.18;0.18;0.18	5.3	5.3	0.74995	Glycosyl transferase, family 2 (1);	0.043508	0.85682	D	0.000000	T	0.54498	0.1862	L	0.52905	1.665	0.80722	D	1	P;B	0.42961	0.795;0.188	P;B	0.44477	0.451;0.172	T	0.55711	-0.8098	10	0.40728	T	0.16	.	8.8658	0.35284	0.9146:0.0:0.0854:0.0	.	189;151	Q10471;G3V1S6	GALT2_HUMAN;.	T	151;189;70;99	ENSP00000445017:K151T;ENSP00000355632:K189T;ENSP00000444346:K99T	ENSP00000355632:K189T	K	+	2	0	GALNT2	228439053	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.149000	0.71795	1.996000	0.58369	0.459000	0.35465	AAA		0.408	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481	
RYR2	6262	hgsc.bcm.edu	37	1	237778016	237778016	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:237778016C>T	ENST00000366574.2	+	37	5905	c.5588C>T	c.(5587-5589)aCg>aTg	p.T1863M	RYR2_ENST00000360064.6_Missense_Mutation_p.T1861M|RYR2_ENST00000542537.1_Missense_Mutation_p.T1847M	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1863	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GAGAGTGACACGCTGGAGAAA	0.542																																																	0			1											55.0	57.0	56.0					1																	237778016		2041	4192	6233	235844639	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.5588C>T	1.37:g.237778016C>T	ENSP00000355533:p.Thr1863Met		235844639	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	3.546	-0.092632	0.07053	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;T;T	0.72835	-0.69;-0.69;-0.69	5.62	-2.98	0.05513	.	1.479610	0.04626	N	0.402749	T	0.46034	0.1372	N	0.08118	0	0.09310	N	1	B	0.22414	0.069	B	0.18561	0.022	T	0.29150	-1.0021	10	0.51188	T	0.08	.	3.2066	0.06667	0.1124:0.2428:0.112:0.5327	.	1863	Q92736	RYR2_HUMAN	M	1863;1861;1847	ENSP00000355533:T1863M;ENSP00000353174:T1861M;ENSP00000443798:T1847M	ENSP00000353174:T1861M	T	+	2	0	RYR2	235844639	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.422000	0.07043	-0.524000	0.06400	0.650000	0.86243	ACG		0.542	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
PLD5	200150	hgsc.bcm.edu	37	1	242383406	242383406	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:242383406T>C	ENST00000536534.2	-	5	860	c.619A>G	c.(619-621)Acg>Gcg	p.T207A	PLD5_ENST00000442594.2_Missense_Mutation_p.T115A|PLD5_ENST00000427495.1_Missense_Mutation_p.T145A			Q8N7P1	PLD5_HUMAN	phospholipase D family, member 5	207						integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(22)|ovary(6)|skin(3)|urinary_tract(1)	55	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			TTCATGTACGTCACCTCGGCT	0.552																																																	0			1											131.0	118.0	122.0					1																	242383406		2203	4300	6503	240450029	SO:0001583	missense	200150			AK098092	CCDS1621.1, CCDS1621.2, CCDS55692.1	1q43	2008-02-05			ENSG00000180287	ENSG00000180287			26879	protein-coding gene	gene with protein product							Standard	NM_001195811		Approved	FLJ40773	uc001hzn.2	Q8N7P1	OTTHUMG00000039867	ENST00000536534.2:c.619A>G	1.37:g.242383406T>C	ENSP00000440896:p.Thr207Ala		240450029	A1KXV0|B7Z324|Q494U9|Q8NB22	Missense_Mutation	SNP	ENST00000536534.2	37	CCDS1621.2	.	.	.	.	.	.	.	.	.	.	T	12.33	1.905769	0.33628	.	.	ENSG00000180287	ENST00000427495;ENST00000442594;ENST00000536534	T;T;T	0.13196	2.61;2.61;2.61	5.52	5.52	0.82312	.	0.238118	0.43747	D	0.000527	T	0.09642	0.0237	N	0.17474	0.49	0.32535	N	0.534433	B;B;B	0.24920	0.114;0.07;0.114	B;B;B	0.24394	0.053;0.024;0.036	T	0.08472	-1.0720	10	0.41790	T	0.15	-20.8238	12.0198	0.53337	0.0:0.0:0.0:1.0	.	115;207;145	Q8N7P1-2;Q8N7P1;Q8N7P1-4	.;PLD5_HUMAN;.	A	145;115;207	ENSP00000401285:T145A;ENSP00000414188:T115A;ENSP00000440896:T207A	ENSP00000401285:T145A	T	-	1	0	PLD5	240450029	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.781000	0.47750	2.093000	0.63338	0.533000	0.62120	ACG		0.552	PLD5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397213.2	NM_152666	
OR2W5	441932	hgsc.bcm.edu	37	1	247654838	247654838	+	RNA	SNP	C	C	T	rs370367058		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:247654838C>T	ENST00000522351.1	+	0	469							A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W, member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R137C(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(24)|ovary(1)|skin(4)	39	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			GGCAGTCATGCGCCCACATCT	0.597																																																	1	Substitution - Missense(1)	breast(1)	1						C	CYS/ARG	0,4406		0,0,2203	113.0	85.0	94.0		409	1.9	0.5	1		94	2,8598	2.2+/-6.3	0,2,4298	no	missense	OR2W5	NM_001004698.2	180	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging	137/321	247654838	2,13004	2203	4300	6503	245721461			441932					1q44	2013-03-27		2004-03-10	ENSG00000203664	ENSG00000203664		"""GPCR / Class A : Olfactory receptors"""	15424	other	unknown				OR2W5P		12213199	Standard	NM_001004698		Approved	OST722	uc001icz.2	A6NFC9	OTTHUMG00000040573		1.37:g.247654838C>T			245721461	B9EH85	Missense_Mutation	SNP	ENST00000522351.1	37																																																																																					0.597	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698	
OR2M3	127062	hgsc.bcm.edu	37	1	248366766	248366766	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:248366766A>G	ENST00000456743.1	+	1	435	c.397A>G	c.(397-399)Acc>Gcc	p.T133A		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	133						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|large_intestine(4)|lung(33)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	50	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TCTAAGATACACCAATCTCAT	0.423																																																	0			1											222.0	222.0	222.0					1																	248366766		2203	4300	6503	246433389	SO:0001583	missense	127062				CCDS31107.1	1q44	2012-08-09		2004-03-10	ENSG00000228198	ENSG00000228198		"""GPCR / Class A : Olfactory receptors"""	8269	protein-coding gene	gene with protein product				OR2M6, OR2M3P			Standard	NM_001004689		Approved	OST003	uc010pzg.2	Q8NG83	OTTHUMG00000040459	ENST00000456743.1:c.397A>G	1.37:g.248366766A>G	ENSP00000389625:p.Thr133Ala		246433389	B9EH06|Q6IEY0	Missense_Mutation	SNP	ENST00000456743.1	37	CCDS31107.1	.	.	.	.	.	.	.	.	.	.	A	7.199	0.593186	0.13875	.	.	ENSG00000228198	ENST00000456743	T	0.19250	2.16	2.55	-5.09	0.02920	GPCR, rhodopsin-like superfamily (1);	0.669759	0.11450	U	0.562904	T	0.10465	0.0256	N	0.25647	0.755	0.09310	N	1	B	0.16396	0.017	B	0.23275	0.045	T	0.27773	-1.0064	10	0.54805	T	0.06	.	1.6802	0.02830	0.4627:0.1774:0.2449:0.115	.	133	Q8NG83	OR2M3_HUMAN	A	133	ENSP00000389625:T133A	ENSP00000389625:T133A	T	+	1	0	OR2M3	246433389	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-10.897000	0.00005	-1.107000	0.03004	-0.842000	0.03052	ACC		0.423	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689	
OR2M4	26245	hgsc.bcm.edu	37	1	248403107	248403107	+	Missense_Mutation	SNP	C	C	T	rs531102387		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:248403107C>T	ENST00000306687.1	+	1	877	c.877C>T	c.(877-879)Cgc>Tgc	p.R293C		NM_017504.1	NP_059974.1	Q96R27	OR2M4_HUMAN	olfactory receptor, family 2, subfamily M, member 4	293					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R293C(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(27)|skin(3)|upper_aerodigestive_tract(2)	50	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TTATAGCCTCCGCAACAAAGA	0.438													c|||	1	0.000199681	0.0	0.0	5008	,	,		18194	0.001		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	large_intestine(1)	1											79.0	73.0	75.0					1																	248403107		2203	4300	6503	246469730	SO:0001583	missense	26245			X64992	CCDS31108.1	1q44	2012-08-09			ENSG00000171180	ENSG00000171180		"""GPCR / Class A : Olfactory receptors"""	8270	protein-coding gene	gene with protein product						1370859, 9119360	Standard	NM_017504		Approved	HTPCRX18, TPCR100, HSHTPCRX18, OST710	uc010pzh.2	Q96R27	OTTHUMG00000040456	ENST00000306687.1:c.877C>T	1.37:g.248403107C>T	ENSP00000306688:p.Arg293Cys		246469730	Q15611|Q8NG82	Missense_Mutation	SNP	ENST00000306687.1	37	CCDS31108.1	.	.	.	.	.	.	.	.	.	.	c	8.596	0.885645	0.17540	.	.	ENSG00000171180	ENST00000306687	T	0.40476	1.03	3.34	-0.264	0.12950	.	0.000000	0.37304	N	0.002142	T	0.50888	0.1642	H	0.98027	4.13	0.09310	N	1	B	0.25667	0.131	B	0.21151	0.033	T	0.56080	-0.8038	10	0.72032	D	0.01	.	3.39	0.07285	0.4765:0.2975:0.0:0.2259	.	293	Q96R27	OR2M4_HUMAN	C	293	ENSP00000306688:R293C	ENSP00000306688:R293C	R	+	1	0	OR2M4	246469730	0.000000	0.05858	0.070000	0.20053	0.811000	0.45836	0.091000	0.15046	0.175000	0.19841	0.543000	0.68304	CGC		0.438	OR2M4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097352.1	NM_017504	
IGF2	3481	hgsc.bcm.edu	37	11	2154760	2154760	+	Missense_Mutation	SNP	G	G	A	rs143785521		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:2154760G>A	ENST00000416167.2	-	3	1459	c.293C>T	c.(292-294)cCg>cTg	p.P98L	IGF2_ENST00000434045.2_Missense_Mutation_p.P154L|IGF2_ENST00000418738.2_Missense_Mutation_p.P98L|IGF2_ENST00000300632.5_Missense_Mutation_p.P98L|IGF2_ENST00000381406.4_Missense_Mutation_p.P101L|IGF2_ENST00000381392.1_Missense_Mutation_p.P101L|IGF2_ENST00000381389.1_Missense_Mutation_p.P98L|MIR483_ENST00000385070.1_RNA|IGF2_ENST00000381395.1_Missense_Mutation_p.P98L			P01344	IGF2_HUMAN	insulin-like growth factor 2	98					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|exocrine pancreas development (GO:0031017)|female pregnancy (GO:0007565)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|organ morphogenesis (GO:0009887)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to nicotine (GO:0035094)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|striated muscle cell differentiation (GO:0051146)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	growth factor activity (GO:0008083)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|protein serine/threonine kinase activator activity (GO:0043539)|receptor activator activity (GO:0030546)			central_nervous_system(1)|kidney(1)|lung(1)|pancreas(1)|skin(1)|urinary_tract(1)	6		all_epithelial(84;5.04e-06)|Breast(177;0.000777)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)	Colorectal(5;0.0179)|COAD - Colon adenocarcinoma(6;0.029)	BRCA - Breast invasive adenocarcinoma(625;1.09e-05)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.153)		AAGCACGGTCGGAGGGGTCGA	0.637																																																	0			11							LEU/PRO,LEU/PRO,LEU/PRO	0,4404		0,0,2202	41.0	37.0	38.0		293,293,461	-0.9	0.0	11	dbSNP_134	38	1,8593	1.2+/-3.3	0,1,4296	no	missense,missense,missense	IGF2	NM_000612.4,NM_001007139.4,NM_001127598.1	98,98,98	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	98/181,98/181,154/237	2154760	1,12997	2202	4297	6499	2111336	SO:0001583	missense	3481			M29645, AK025719	CCDS7728.1, CCDS44517.1	11p15.5	2014-09-16	2014-09-16		ENSG00000167244	ENSG00000167244			5466	protein-coding gene	gene with protein product	"""somatomedin A"""	147470	"""chromosome 11 open reading frame 43"""	C11orf43		2450353, 3167054	Standard	NM_000612		Approved	FLJ44734, IGF-II	uc009ydf.3	P01344	OTTHUMG00000009395	ENST00000416167.2:c.293C>T	11.37:g.2154760G>A	ENSP00000414497:p.Pro98Leu		2111336	B3KX48|B7WP08|C9JAF2|E3UN45|P78449|Q14299|Q1WM26|Q9UC68|Q9UC69	Missense_Mutation	SNP	ENST00000416167.2	37	CCDS7728.1	.	.	.	.	.	.	.	.	.	.	G	5.251	0.231857	0.09969	0.0	1.16E-4	ENSG00000167244	ENST00000381395;ENST00000381406;ENST00000416167;ENST00000300632;ENST00000381319;ENST00000434045;ENST00000381392;ENST00000381389;ENST00000418738;ENST00000337883;ENST00000381379	D;D;D;D;D;D;D;D;D	0.91740	-2.86;-2.83;-2.86;-2.86;-2.9;-2.83;-2.86;-2.86;-2.86	3.16	-0.938	0.10412	Insulin-like growth factor II E-peptide, C-terminal (1);	0.140501	0.48286	U	0.000182	T	0.82047	0.4952	L	0.27053	0.805	0.37648	D	0.922316	B;B	0.12013	0.005;0.005	B;B	0.04013	0.001;0.001	T	0.66893	-0.5808	10	0.45353	T	0.12	-10.0653	4.4442	0.11589	0.3124:0.0:0.5136:0.1739	.	154;98	C9JAF2;P01344	.;IGF2_HUMAN	L	98;101;98;98;101;154;101;98;98;98;101	ENSP00000370802:P98L;ENSP00000370813:P101L;ENSP00000414497:P98L;ENSP00000300632:P98L;ENSP00000391826:P154L;ENSP00000370799:P101L;ENSP00000370796:P98L;ENSP00000402047:P98L;ENSP00000338297:P98L	ENSP00000300632:P98L	P	-	2	0	IGF2	2111336	1.000000	0.71417	0.011000	0.14972	0.962000	0.63368	2.245000	0.43133	-0.228000	0.09869	0.450000	0.29827	CCG		0.637	IGF2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026053.2	NM_000612	
OR51E2	81285	hgsc.bcm.edu	37	11	4703580	4703580	+	Missense_Mutation	SNP	C	C	T	rs201184158		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:4703580C>T	ENST00000396950.3	-	2	601	c.362G>A	c.(361-363)cGt>cAt	p.R121H		NM_030774.3	NP_110401.1	Q9H255	O51E2_HUMAN	olfactory receptor, family 51, subfamily E, member 2	121					cellular response to fatty acid (GO:0071398)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|positive regulation of blood pressure (GO:0045777)|positive regulation of renin secretion into blood stream (GO:1900135)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|signaling receptor activity (GO:0038023)|steroid hormone receptor activity (GO:0003707)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(3)	23		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;3e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00476)|LUSC - Lung squamous cell carcinoma(625;0.2)		GGCCACATAACGGTCAAAGGC	0.537																																																	0			11											60.0	49.0	52.0					11																	4703580		2201	4298	6499	4660156	SO:0001583	missense	81285			AY033942	CCDS7751.1	11p15	2012-08-09			ENSG00000167332	ENSG00000167332		"""GPCR / Class A : Olfactory receptors"""	15195	protein-coding gene	gene with protein product		611268				11118034	Standard	NM_030774		Approved	PSGR	uc001lzk.2	Q9H255	OTTHUMG00000133362	ENST00000396950.3:c.362G>A	11.37:g.4703580C>T	ENSP00000380153:p.Arg121His		4660156	B2RA63|Q6IF94	Missense_Mutation	SNP	ENST00000396950.3	37	CCDS7751.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.415059	0.83449	.	.	ENSG00000167332	ENST00000396950	T	0.77489	-1.1	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42964	D	0.000632	D	0.90300	0.6966	H	0.94734	3.575	0.44337	D	0.99722	D	0.89917	1.0	D	0.91635	0.999	D	0.91843	0.5485	10	0.72032	D	0.01	.	11.3906	0.49811	0.0:0.9131:0.0:0.0869	.	121	Q9H255	O51E2_HUMAN	H	121	ENSP00000380153:R121H	ENSP00000380153:R121H	R	-	2	0	OR51E2	4660156	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.693000	0.68264	2.613000	0.88420	0.655000	0.94253	CGT		0.537	OR51E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257198.1	NM_030774	
OVCH2	341277	hgsc.bcm.edu	37	11	7720314	7720314	+	RNA	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:7720314C>T	ENST00000534193.2	-	0	934				OVCH2_ENST00000454689.1_RNA			Q7RTZ1	OVCH2_HUMAN	ovochymase 2 (gene/pseudogene)							extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			cervix(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(2)	15				Epithelial(150;7.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.197)		GCTCTTTCTCCGATTACCTGG	0.448																																																	0			11											52.0	53.0	53.0					11																	7720314		1838	4080	5918	7676890			341277			BN000120	CCDS73251.1	11p15.4	2012-10-02	2010-06-08		ENSG00000183378	ENSG00000183378			29970	protein-coding gene	gene with protein product			"""ovochymase 2"""			12838346	Standard	XM_006718221		Approved	OVTN	uc031pyw.1	Q7RTZ1	OTTHUMG00000165418		11.37:g.7720314C>T			7676890		Missense_Mutation	SNP	ENST00000534193.2	37		.	.	.	.	.	.	.	.	.	.	C	0.013	-1.615665	0.00828	.	.	ENSG00000183378	ENST00000454689	D	0.86230	-2.09	4.32	-8.65	0.00870	.	1.683680	0.03838	N	0.270061	T	0.75903	0.3913	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.64664	-0.6354	10	0.09590	T	0.72	0.9161	12.8624	0.57922	0.1019:0.6899:0.0:0.2082	.	303	Q7RTZ1	OVCH2_HUMAN	Q	303	ENSP00000407158:R303Q	ENSP00000407158:R303Q	R	-	2	0	OVCH2	7676890	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.087000	0.00610	-2.862000	0.00326	-0.813000	0.03139	CGG		0.448	OVCH2-001	KNOWN	non_canonical_polymorphism|not_organism_supported|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000383929.7	NM_198185	
COMMD9	29099	hgsc.bcm.edu	37	11	36296289	36296289	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:36296289G>A	ENST00000263401.5	-	6	506	c.490C>T	c.(490-492)Ccc>Tcc	p.P164S	COMMD9_ENST00000533308.1_5'Flank|COMMD9_ENST00000532705.1_Missense_Mutation_p.T152I|LINC00610_ENST00000355500.1_lincRNA|COMMD9_ENST00000452374.2_Missense_Mutation_p.P122S	NM_014186.3	NP_054905.2	Q9P000	COMD9_HUMAN	COMM domain containing 9	164	COMM. {ECO:0000255|PROSITE- ProRule:PRU00602}.									kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	5	all_lung(20;0.211)	all_hematologic(20;0.107)				GAGATGGAGGGTTTGTCTCCG	0.542																																																	0			11											151.0	124.0	133.0					11																	36296289		2202	4298	6500	36252865	SO:0001583	missense	29099			AY542164	CCDS7900.1, CCDS44571.1	11p13	2008-02-05			ENSG00000110442	ENSG00000110442			25014	protein-coding gene	gene with protein product		612299				15799966	Standard	NM_014186		Approved	HSPC166, FLJ31106	uc001mwn.4	Q9P000	OTTHUMG00000166333	ENST00000263401.5:c.490C>T	11.37:g.36296289G>A	ENSP00000263401:p.Pro164Ser		36252865	E9PAN2|Q96FI2|Q9H0R0	Missense_Mutation	SNP	ENST00000263401.5	37	CCDS7900.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.847|9.847	1.192681|1.192681	0.21954|0.21954	.|.	.|.	ENSG00000110442|ENSG00000110442	ENST00000263401;ENST00000537683;ENST00000452374|ENST00000532705	T;T|.	0.09350|.	2.99;2.99|.	5.66|5.66	4.75|4.75	0.60458|0.60458	COMM domain (1);|.	0.290765|.	0.38605|.	N|.	0.001634|.	T|T	0.55924|0.55924	0.1951|0.1951	M|M	0.74258|0.74258	2.255|2.255	0.09310|0.09310	N|N	1|1	P;P|.	0.49783|.	0.928;0.669|.	B;B|.	0.44108|.	0.441;0.355|.	T|T	0.49173|0.49173	-0.8967|-0.8967	10|6	0.35671|0.34782	T|T	0.21|0.22	-18.0524|-18.0524	10.1884|10.1884	0.43011|0.43011	0.159:0.0:0.841:0.0|0.159:0.0:0.841:0.0	.|.	122;164|.	Q9P000-2;Q9P000|.	.;COMD9_HUMAN|.	S|I	164;164;122|152	ENSP00000263401:P164S;ENSP00000392510:P122S|.	ENSP00000263401:P164S|ENSP00000435599:T152I	P|T	-|-	1|2	0|0	COMMD9|COMMD9	36252865|36252865	0.985000|0.985000	0.35326|0.35326	0.362000|0.362000	0.25862|0.25862	0.810000|0.810000	0.45777|0.45777	3.175000|3.175000	0.50855|0.50855	1.386000|1.386000	0.46466|0.46466	0.655000|0.655000	0.94253|0.94253	CCC|ACC		0.542	COMMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389196.1	NM_014186	
SLC22A11	55867	hgsc.bcm.edu	37	11	64323797	64323797	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:64323797A>G	ENST00000301891.4	+	1	700	c.326A>G	c.(325-327)gAc>gGc	p.D109G	SLC22A11_ENST00000490834.1_3'UTR|SLC22A11_ENST00000377581.3_Missense_Mutation_p.D109G|SLC22A11_ENST00000377585.3_Missense_Mutation_p.D109G	NM_018484.2	NP_060954.1	Q9NSA0	S22AB_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 11	109					organic anion transport (GO:0015711)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23					Aminohippurate(DB00345)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Estradiol(DB00783)|Furosemide(DB00695)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Novobiocin(DB01051)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Salicylic acid(DB00936)|Tetracycline(DB00759)|Zidovudine(DB00495)	AGCGAAGCTGACACGGAGCCG	0.682																																																	0			11											46.0	52.0	50.0					11																	64323797		2201	4297	6498	64080373	SO:0001583	missense	55867			AB026116	CCDS8074.1	11q13.3	2013-05-22	2008-01-11		ENSG00000168065	ENSG00000168065		"""Solute carriers"""	18120	protein-coding gene	gene with protein product		607097				10660625, 15576633, 17229912	Standard	NM_018484		Approved	OAT4	uc001oai.3	Q9NSA0	OTTHUMG00000045142	ENST00000301891.4:c.326A>G	11.37:g.64323797A>G	ENSP00000301891:p.Asp109Gly		64080373	A8K426|Q53GR2|Q6ZP72|Q8NBU4	Missense_Mutation	SNP	ENST00000301891.4	37	CCDS8074.1	.	.	.	.	.	.	.	.	.	.	A	4.244	0.044209	0.08196	.	.	ENSG00000168065	ENST00000301891;ENST00000377585;ENST00000377581	T;T;T	0.15487	2.42;2.42;2.42	3.97	-5.2	0.02823	Major facilitator superfamily domain (1);	0.488989	0.20471	U	0.091696	T	0.17874	0.0429	N	0.25332	0.735	0.09310	N	1	B;B;B;D	0.53619	0.027;0.009;0.034;0.961	B;B;B;P	0.56216	0.013;0.022;0.022;0.794	T	0.10291	-1.0636	10	0.25751	T	0.34	.	16.0505	0.80760	0.8333:0.1667:0.0:0.0	.	109;109;109;109	Q9NSA0-2;A6NCG2;Q9NSA0;B4DJH6	.;.;S22AB_HUMAN;.	G	109	ENSP00000301891:D109G;ENSP00000366809:D109G;ENSP00000366804:D109G	ENSP00000301891:D109G	D	+	2	0	SLC22A11	64080373	0.002000	0.14202	0.001000	0.08648	0.002000	0.02628	0.014000	0.13333	-0.693000	0.05121	-0.565000	0.04167	GAC		0.682	SLC22A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104886.4	NM_018484	
MRGPRD	116512	hgsc.bcm.edu	37	11	68748293	68748293	+	Nonsense_Mutation	SNP	G	G	A	rs140992386		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:68748293G>A	ENST00000309106.3	-	1	162	c.163C>T	c.(163-165)Cga>Tga	p.R55*		NM_198923.2	NP_944605.2	Q8TDS7	MRGRD_HUMAN	MAS-related GPR, member D	55						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)	22			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CTGTGCATTCGAAAGCCCAGC	0.597																																																	0			11						G	stop/ARG	0,4400		0,0,2200	66.0	66.0	66.0		163	-5.3	0.0	11	dbSNP_134	66	1,8587	1.2+/-3.3	0,1,4293	yes	stop-gained	MRGPRD	NM_198923.2		0,1,6493	AA,AG,GG		0.0116,0.0,0.0077		55/322	68748293	1,12987	2200	4294	6494	68504869	SO:0001587	stop_gained	116512			AB083627	CCDS31625.1	11q13.3	2012-08-21			ENSG00000172938	ENSG00000172938		"""GPCR / Class A : Orphans"""	29626	protein-coding gene	gene with protein product		607231				11551509, 12909716	Standard	NM_198923		Approved	mrgD	uc010rqf.2	Q8TDS7	OTTHUMG00000167896	ENST00000309106.3:c.163C>T	11.37:g.68748293G>A	ENSP00000310631:p.Arg55*		68504869	Q8NGK7	Nonsense_Mutation	SNP	ENST00000309106.3	37	CCDS31625.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.520969	0.44866	0.0	1.16E-4	ENSG00000172938	ENST00000309106	.	.	.	5.17	-5.33	0.02713	.	0.603819	0.13615	U	0.374820	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.3184	0.723	0.00944	0.3441:0.104:0.2356:0.3163	.	.	.	.	X	55	.	ENSP00000310631:R55X	R	-	1	2	MRGPRD	68504869	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.442000	0.06871	-0.996000	0.03455	-0.373000	0.07131	CGA		0.597	MRGPRD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396874.1	NM_198923	
C11orf30	56946	hgsc.bcm.edu	37	11	76169374	76169374	+	Silent	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:76169374A>G	ENST00000529032.1	+	4	393	c.393A>G	c.(391-393)ccA>ccG	p.P131P	C11orf30_ENST00000334736.3_Silent_p.P131P|C11orf30_ENST00000525038.1_Silent_p.P145P|C11orf30_ENST00000524490.1_Silent_p.P131P|C11orf30_ENST00000533248.1_Silent_p.P145P|C11orf30_ENST00000343878.3_Silent_p.P131P|C11orf30_ENST00000524767.1_Silent_p.P145P|C11orf30_ENST00000525919.1_Silent_p.P131P			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	131	Interaction with BRCA2.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						CATCTCTTCCAGTGCCTGCAG	0.428																																																	0			11											87.0	85.0	86.0					11																	76169374		2200	4292	6492	75847022	SO:0001819	synonymous_variant	56946			AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.393A>G	11.37:g.76169374A>G			75847022	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Silent	SNP	ENST00000529032.1	37	CCDS8244.1																																																																																				0.428	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193	
ATM	472	hgsc.bcm.edu	37	11	108236086	108236086	+	Missense_Mutation	SNP	C	C	A	rs587782292		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:108236086C>A	ENST00000452508.2	+	64	9211	c.9022C>A	c.(9022-9024)Cgt>Agt	p.R3008S	ATM_ENST00000525178.1_3'UTR|C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.R3008S|C11orf65_ENST00000526725.1_Intron			Q13315	ATM_HUMAN	ATM serine/threonine kinase	3008			R -> C (in AT, T-prolymphocytic leukemia and mantle cell lymphoma). {ECO:0000269|PubMed:10706620, ECO:0000269|PubMed:10817650, ECO:0000269|PubMed:9334731, ECO:0000269|PubMed:9488043, ECO:0000269|PubMed:9872980}.|R -> H (in B-cell chronic lymphocytic leukemia). {ECO:0000269|PubMed:10397742}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.R3008C(4)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	AGTAGCTGAACGTGTCTTAAT	0.413			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																													yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	4	Substitution - Missense(4)	haematopoietic_and_lymphoid_tissue(4)	11	GRCh37	CM000656	ATM	M							127.0	124.0	125.0					11																	108236086		2201	4298	6499	107741296	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.9022C>A	11.37:g.108236086C>A	ENSP00000388058:p.Arg3008Ser		107741296	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.011988	0.75046	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.02121	4.44;4.44	5.22	5.22	0.72569	Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.110750	0.64402	D	0.000007	T	0.14098	0.0341	M	0.81497	2.545	0.80722	D	1	D	0.76494	0.999	D	0.68943	0.961	T	0.00083	-1.2103	10	0.87932	D	0	.	19.0354	0.92974	0.0:1.0:0.0:0.0	.	3008	Q13315	ATM_HUMAN	S	3008	ENSP00000278616:R3008S;ENSP00000388058:R3008S	ENSP00000278616:R3008S	R	+	1	0	ATM	107741296	1.000000	0.71417	0.998000	0.56505	0.549000	0.35272	5.681000	0.68175	2.726000	0.93360	0.650000	0.86243	CGT		0.413	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
EXPH5	23086	hgsc.bcm.edu	37	11	108385374	108385374	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:108385374A>G	ENST00000265843.4	-	6	970	c.860T>C	c.(859-861)tTt>tCt	p.F287S	EXPH5_ENST00000428840.1_Missense_Mutation_p.F211S|EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000443411.1_Missense_Mutation_p.F99S|EXPH5_ENST00000525344.1_Missense_Mutation_p.F280S	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	287					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)	p.F287S(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CCTAGGAGAAAAGGTTTTAAA	0.363																																																	1	Substitution - Missense(1)	ovary(1)	11											95.0	90.0	92.0					11																	108385374		2201	4298	6499	107890584	SO:0001583	missense	23086				CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.860T>C	11.37:g.108385374A>G	ENSP00000265843:p.Phe287Ser		107890584	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	A	17.73	3.460487	0.63401	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.06294	3.92;3.83;3.69;3.92;3.73;3.32	5.67	5.67	0.87782	.	0.105878	0.42548	D	0.000685	T	0.19446	0.0467	M	0.69823	2.125	0.31610	N	0.651609	D	0.89917	1.0	D	0.85130	0.997	T	0.26710	-1.0095	10	0.66056	D	0.02	-20.0778	5.0773	0.14638	0.708:0.1762:0.1158:0.0	.	287	Q8NEV8	EXPH5_HUMAN	S	287;211;99;280;131;211;99	ENSP00000265843:F287S;ENSP00000391966:F211S;ENSP00000411390:F99S;ENSP00000432546:F280S;ENSP00000432683:F211S;ENSP00000446434:F99S	ENSP00000265843:F287S	F	-	2	0	EXPH5	107890584	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.272000	0.51616	2.154000	0.67381	0.533000	0.62120	TTT		0.363	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
BCL9L	283149	hgsc.bcm.edu	37	11	118771916	118771916	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:118771916G>A	ENST00000334801.3	-	6	3500	c.2536C>T	c.(2536-2538)Cag>Tag	p.Q846*	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	846					canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		AATCCCTGCTGGCCCTGGTTG	0.602																																																	0			11											84.0	76.0	79.0					11																	118771916		2200	4295	6495	118277126	SO:0001587	stop_gained	283149			AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.2536C>T	11.37:g.118771916G>A	ENSP00000335320:p.Gln846*		118277126	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Nonsense_Mutation	SNP	ENST00000334801.3	37	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	G	47	13.396728	0.99739	.	.	ENSG00000186174	ENST00000334801;ENST00000526143;ENST00000525300;ENST00000392849;ENST00000431085	.	.	.	5.11	4.19	0.49359	.	0.000000	0.47455	D	0.000235	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	-11.3315	4.6956	0.12802	0.0829:0.1513:0.6097:0.1561	.	.	.	.	X	846;809;139;846;846	.	ENSP00000335320:Q846X	Q	-	1	0	BCL9L	118277126	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.327000	0.52045	2.358000	0.79984	0.655000	0.94253	CAG		0.602	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557	
OR8A1	390275	hgsc.bcm.edu	37	11	124440424	124440424	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:124440424T>C	ENST00000284287.3	+	1	532	c.460T>C	c.(460-462)Tct>Cct	p.S154P		NM_001005194.1	NP_001005194.1	Q8NGG7	OR8A1_HUMAN	olfactory receptor, family 8, subfamily A, member 1	154					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			haematopoietic_and_lymphoid_tissue(1)|lung(16)|ovary(2)|prostate(1)|skin(2)	22		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0214)		CATCATTATGTCTCATCACAC	0.483																																																	0			11											161.0	135.0	144.0					11																	124440424		2201	4299	6500	123945634	SO:0001583	missense	390275			BK004495	CCDS31712.1	11q24.2	2012-08-09			ENSG00000196119	ENSG00000196119		"""GPCR / Class A : Olfactory receptors"""	8469	protein-coding gene	gene with protein product							Standard	NM_001005194		Approved	OST025	uc010san.2	Q8NGG7	OTTHUMG00000165923	ENST00000284287.3:c.460T>C	11.37:g.124440424T>C	ENSP00000284287:p.Ser154Pro		123945634	Q6IEW7|Q96RC6	Missense_Mutation	SNP	ENST00000284287.3	37	CCDS31712.1	.	.	.	.	.	.	.	.	.	.	T	14.65	2.598616	0.46318	.	.	ENSG00000196119	ENST00000284287	T	0.41065	1.01	5.03	3.89	0.44902	GPCR, rhodopsin-like superfamily (1);	0.309751	0.23364	N	0.048991	T	0.46698	0.1406	M	0.88031	2.925	0.29436	N	0.859502	B	0.21905	0.062	B	0.30316	0.114	T	0.56673	-0.7940	10	0.72032	D	0.01	.	2.3025	0.04165	0.1446:0.0825:0.2826:0.4903	.	154	Q8NGG7	OR8A1_HUMAN	P	154	ENSP00000284287:S154P	ENSP00000284287:S154P	S	+	1	0	OR8A1	123945634	0.028000	0.19301	0.921000	0.36526	0.670000	0.39368	-0.007000	0.12810	0.905000	0.36596	0.528000	0.53228	TCT		0.483	OR8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387062.1	NM_001005194	
MUC21	394263	hgsc.bcm.edu	37	6	30954921	30954921	+	Silent	SNP	C	C	G	rs548248760	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr6:30954921C>G	ENST00000376296.3	+	2	1210	c.969C>G	c.(967-969)acC>acG	p.T323T	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	323	28 X 15 AA approximate tandem repeats.|Ser-rich.		T -> P (in dbSNP:rs41288679). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14574404}.		cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CCAGCACAACCTCCAGTGGGG	0.627													c|||	32	0.00638978	0.0083	0.0144	5008	,	,		22635	0.001		0.005	False		,,,				2504	0.0051																0			6																																								31062900	SO:0001819	synonymous_variant	394263			AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.969C>G	6.37:g.30954921C>G			31062900	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																				0.627	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
RNF8	9025	hgsc.bcm.edu	37	6	37358529	37358529	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr6:37358529T>C	ENST00000373479.4	+	8	1646	c.1453T>C	c.(1453-1455)Ttc>Ctc	p.F485L	RNF8_ENST00000469731.1_Silent_p.C416C	NM_003958.3|NM_183078.2	NP_003949.1|NP_898901.1	O76064	RNF8_HUMAN	ring finger protein 8, E3 ubiquitin protein ligase	485					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|histone exchange (GO:0043486)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A ubiquitination (GO:0033522)|histone H2B ubiquitination (GO:0033523)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|mitotic nuclear division (GO:0007067)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|response to ionizing radiation (GO:0010212)|spermatid development (GO:0007286)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome, telomeric region (GO:0000781)|nucleolus (GO:0005730)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	13						AAAGAGATTGTTCTGAAGACC	0.502																																																	0			6											113.0	110.0	111.0					6																	37358529		2203	4300	6503	37466507	SO:0001583	missense	9025			AB012770	CCDS4833.1, CCDS4834.1	6p21.3	2013-01-09	2012-02-23		ENSG00000112130	ENSG00000112130		"""RING-type (C3HC4) zinc fingers"""	10071	protein-coding gene	gene with protein product		611685	"""ring finger protein (C3HC4 type) 8"", ""ring finger protein 8"""			9734811, 9852682	Standard	NM_003958		Approved	KIAA0646	uc003onq.4	O76064	OTTHUMG00000014620	ENST00000373479.4:c.1453T>C	6.37:g.37358529T>C	ENSP00000362578:p.Phe485Leu		37466507	A6NN24|A8MYC0|B4DPG0|Q53H16|Q5NKW5	Missense_Mutation	SNP	ENST00000373479.4	37	CCDS4834.1	.	.	.	.	.	.	.	.	.	.	T	11.07	1.530486	0.27387	.	.	ENSG00000112130	ENST00000373479;ENST00000498460	D	0.84442	-1.85	5.02	3.85	0.44370	.	0.700839	0.13829	N	0.359888	T	0.60470	0.2271	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.54951	-0.8216	9	0.23302	T	0.38	.	7.5659	0.27879	0.0:0.0965:0.0:0.9035	.	485	O76064	RNF8_HUMAN	L	485;176	ENSP00000362578:F485L	ENSP00000362578:F485L	F	+	1	0	RNF8	37466507	0.003000	0.15002	0.860000	0.33809	0.569000	0.35902	1.059000	0.30517	1.033000	0.39918	0.533000	0.62120	TTC		0.502	RNF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040403.2		
TJAP1	93643	hgsc.bcm.edu	37	6	43466758	43466758	+	Missense_Mutation	SNP	G	G	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr6:43466758G>C	ENST00000372445.5	+	4	395	c.19G>C	c.(19-21)Gct>Cct	p.A7P	TJAP1_ENST00000372452.1_Missense_Mutation_p.A7P|TJAP1_ENST00000372449.1_Missense_Mutation_p.A7P|TJAP1_ENST00000483640.1_3'UTR|TJAP1_ENST00000436109.2_Missense_Mutation_p.A7P|TJAP1_ENST00000259751.1_Missense_Mutation_p.A7P|TJAP1_ENST00000438588.2_Missense_Mutation_p.A7P|TJAP1_ENST00000372444.2_Missense_Mutation_p.A7P	NM_001146016.1	NP_001139488.1	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 (peripheral)	7					Golgi organization (GO:0007030)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|urinary_tract(2)	21	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			TGCCGCCCCTGCTAAGAAACC	0.582																																																	0			6											84.0	70.0	75.0					6																	43466758		2203	4300	6503	43574736	SO:0001583	missense	93643			AK024269	CCDS4898.1, CCDS55004.1	6p21.1	2008-02-05	2005-07-05	2005-07-05	ENSG00000137221	ENSG00000137221			17949	protein-coding gene	gene with protein product		612658	"""tight junction protein 4 (peripheral)"""	TJP4		11602598	Standard	NM_001146016		Approved	PILT	uc011dvh.1	Q5JTD0	OTTHUMG00000014736	ENST00000372445.5:c.19G>C	6.37:g.43466758G>C	ENSP00000361522:p.Ala7Pro		43574736	Q05BH9|Q5JTD1|Q5JWW1|Q68DB2|Q6P2P3|Q9H7V7	Missense_Mutation	SNP	ENST00000372445.5	37	CCDS55004.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.835493	0.50951	.	.	ENSG00000137221	ENST00000372444;ENST00000372445;ENST00000436109;ENST00000442878;ENST00000259751;ENST00000372454;ENST00000372452;ENST00000372449;ENST00000438588	T;T;T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91	5.31	4.36	0.52297	.	0.275252	0.35708	N	0.003033	T	0.21062	0.0507	L	0.40543	1.245	0.40092	D	0.976269	B;P;P	0.45212	0.0;0.853;0.853	B;B;B	0.42882	0.002;0.401;0.401	T	0.10636	-1.0621	10	0.59425	D	0.04	-5.8652	5.9438	0.19207	0.0992:0.0:0.582:0.3188	.	7;7;7	E2QRK7;Q5JTD0;Q5JTD0-2	.;TJAP1_HUMAN;.	P	7	ENSP00000361521:A7P;ENSP00000361522:A7P;ENSP00000407080:A7P;ENSP00000390981:A7P;ENSP00000259751:A7P;ENSP00000361530:A7P;ENSP00000361527:A7P;ENSP00000408769:A7P	ENSP00000259751:A7P	A	+	1	0	TJAP1	43574736	0.896000	0.30565	1.000000	0.80357	0.999000	0.98932	2.092000	0.41700	2.495000	0.84180	0.655000	0.94253	GCT		0.582	TJAP1-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040629.1	NM_080604	
DST	667	hgsc.bcm.edu	37	6	56483974	56483974	+	Missense_Mutation	SNP	C	C	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr6:56483974C>A	ENST00000370765.6	-	23	4965	c.4858G>T	c.(4858-4860)Ggt>Tgt	p.G1620C	DST_ENST00000370769.4_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370754.5_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	6360					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TCTTTAAAACCATCTGCCTGA	0.353																																																	0			6											171.0	166.0	168.0					6																	56483974		2202	4299	6501	56591933	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.4858G>T	6.37:g.56483974C>A	ENSP00000359801:p.Gly1620Cys		56591933	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000370765.6	37	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	C	14.54	2.566457	0.45694	.	.	ENSG00000151914	ENST00000370765	T	0.39592	1.07	5.35	4.25	0.50352	.	.	.	.	.	T	0.39332	0.1074	.	.	.	0.20074	N	0.999932	D	0.63880	0.993	P	0.56514	0.8	T	0.40327	-0.9569	7	0.56958	D	0.05	.	7.7125	0.28686	0.0:0.7506:0.0:0.2494	.	1620	Q03001-3	.	C	1620	ENSP00000359801:G1620C	ENSP00000359801:G1620C	G	-	1	0	DST	56591933	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.311000	0.43717	2.661000	0.90470	0.650000	0.86243	GGT		0.353	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723	
EPHA7	2045	hgsc.bcm.edu	37	6	93965716	93965716	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr6:93965716T>C	ENST00000369303.4	-	13	2396	c.2212A>G	c.(2212-2214)Atg>Gtg	p.M738V		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	738	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		CCTCTCAGCATTCCTACTAAC	0.403																																																	0			6											135.0	130.0	132.0					6																	93965716		2203	4300	6503	94022437	SO:0001583	missense	2045			L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3390	protein-coding gene	gene with protein product		602190	"""EphA7"""			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.2212A>G	6.37:g.93965716T>C	ENSP00000358309:p.Met738Val		94022437	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	37	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.569161	0.86439	.	.	ENSG00000135333	ENST00000369303	T	0.61040	0.14	5.75	5.75	0.90469	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.48187	0.1486	L	0.29908	0.895	0.80722	D	1	P;D;D	0.55385	0.825;0.964;0.971	P;P;P	0.51615	0.629;0.546;0.675	T	0.56153	-0.8026	10	0.72032	D	0.01	.	16.0455	0.80717	0.0:0.0:0.0:1.0	.	734;733;738	Q15375-4;Q15375-2;Q15375	.;.;EPHA7_HUMAN	V	738	ENSP00000358309:M738V	ENSP00000358309:M738V	M	-	1	0	EPHA7	94022437	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.189000	0.69895	0.460000	0.39030	ATG		0.403	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1		
AK9	221264	hgsc.bcm.edu	37	6	109854526	109854526	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr6:109854526T>C	ENST00000424296.2	-	28	3574	c.3498A>G	c.(3496-3498)gaA>gaG	p.E1166E	AK9_ENST00000341338.6_Silent_p.E245E|AK9_ENST00000355283.1_Silent_p.E245E	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	1166	Adenylate kinase 2.				ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)	p.E245E(1)									GTTTCCACTTTTCAATTTGGG	0.358																																																	1	Substitution - coding silent(1)	ovary(1)	6											169.0	151.0	157.0					6																	109854526		2203	4300	6503	109961219	SO:0001819	synonymous_variant	221264			AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.3498A>G	6.37:g.109854526T>C			109961219	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Silent	SNP	ENST00000424296.2	37	CCDS55048.1	.	.	.	.	.	.	.	.	.	.	T	8.653	0.898716	0.17686	.	.	ENSG00000155085	ENST00000470564;ENST00000491875	.	.	.	5.16	-0.0333	0.13901	.	.	.	.	.	T	0.34077	0.0885	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.22941	-1.0202	4	.	.	.	.	4.5933	0.12317	0.1325:0.2279:0.0:0.6396	.	.	.	.	R	4;101	.	.	K	-	2	0	AKD1	109961219	0.456000	0.25744	0.472000	0.27241	0.889000	0.51656	0.241000	0.18065	0.047000	0.15862	0.448000	0.29417	AAA		0.358	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	
TBC1D32	221322	hgsc.bcm.edu	37	6	121638667	121638667	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr6:121638667A>G	ENST00000398212.2	-	3	518	c.469T>C	c.(469-471)Tct>Cct	p.S157P	TBC1D32_ENST00000275159.6_Missense_Mutation_p.S157P	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	157					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										TCACTATCAGAGCAATTGTCT	0.318																																																	0			6											296.0	270.0	278.0					6																	121638667		1862	4091	5953	121680366	SO:0001583	missense	221322			AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.469T>C	6.37:g.121638667A>G	ENSP00000381270:p.Ser157Pro		121680366	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	A	15.56	2.870427	0.51588	.	.	ENSG00000146350	ENST00000275159;ENST00000398212;ENST00000422369	T;T;T	0.25414	1.8;1.8;1.8	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.20170	0.0485	M	0.62016	1.91	0.54753	D	0.999987	P	0.47762	0.9	B	0.43194	0.411	T	0.02805	-1.1108	10	0.51188	T	0.08	-0.0535	15.0687	0.72017	1.0:0.0:0.0:0.0	.	157	Q96NH3	BROMI_HUMAN	P	157	ENSP00000275159:S157P;ENSP00000381270:S157P;ENSP00000397993:S157P	ENSP00000275159:S157P	S	-	1	0	C6orf170	121680366	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	8.050000	0.89445	2.013000	0.59113	0.533000	0.62120	TCT		0.318	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
MAP3K4	4216	hgsc.bcm.edu	37	6	161491657	161491657	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr6:161491657T>C	ENST00000392142.4	+	4	1873	c.1725T>C	c.(1723-1725)gaT>gaC	p.D575D	MAP3K4_ENST00000348824.7_Silent_p.D575D|MAP3K4_ENST00000366919.2_Silent_p.D575D|MAP3K4_ENST00000366920.2_Silent_p.D575D	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	575					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		AATTTCCAGATCCCATGTGGG	0.428																																																	0			6											123.0	122.0	123.0					6																	161491657		2203	4300	6503	161411647	SO:0001819	synonymous_variant	4216			AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.1725T>C	6.37:g.161491657T>C			161411647	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Silent	SNP	ENST00000392142.4	37	CCDS34565.1																																																																																				0.428	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3		
ATP2A3	489	hgsc.bcm.edu	37	17	3844345	3844345	+	Missense_Mutation	SNP	G	G	A	rs9895012	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:3844345G>A	ENST00000352011.3	-	14	2074	c.2020C>T	c.(2020-2022)Cgc>Tgc	p.R674C	ATP2A3_ENST00000397035.3_Missense_Mutation_p.R674C|ATP2A3_ENST00000309890.7_Missense_Mutation_p.R674C|ATP2A3_ENST00000397041.3_Missense_Mutation_p.R674C|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000397043.3_Missense_Mutation_p.R674C|ATP2A3_ENST00000359983.3_Missense_Mutation_p.R674C			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	674			R -> H (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		GCGAAGCAGCGGGCGGTGCGG	0.657													G|||	65	0.0129792	0.0008	0.0259	5008	,	,		13726	0.001		0.0408	False		,,,				2504	0.0041				GBM(32;29 774 15719 37967)												0			17	GRCh37	CM992303	ATP2A3	M	rs9895012	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	23,4383	29.0+/-57.7	0,23,2180	55.0	59.0	58.0		2020,2020,2020,2020,2020,2020,2020	-4.6	0.8	17	dbSNP_119	58	220,8368	86.3+/-148.7	1,218,4075	yes	missense,missense,missense,missense,missense,missense,missense	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	180,180,180,180,180,180,180	1,241,6255	AA,AG,GG		2.5617,0.522,1.8701	benign,benign,benign,benign,benign,benign,benign	674/1000,674/1053,674/1045,674/1044,674/1030,674/999,674/1030	3844345	243,12751	2203	4294	6497	3791094	SO:0001583	missense	489				CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.2020C>T	17.37:g.3844345G>A	ENSP00000301387:p.Arg674Cys		3791094	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Missense_Mutation	SNP	ENST00000352011.3	37	CCDS11041.1	44	0.020146520146520148	0	0.0	13	0.03591160220994475	1	0.0017482517482517483	30	0.0395778364116095	G	11.91	1.778975	0.31502	0.00522	0.025617	ENSG00000074370	ENST00000397043;ENST00000352011;ENST00000359983;ENST00000397041;ENST00000397045;ENST00000309890;ENST00000397035	D;D;D;D;D;D	0.95756	-3.8;-3.8;-3.8;-3.8;-3.8;-3.8	4.16	-4.62	0.03370	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.192116	0.45867	N	0.000325	T	0.78541	0.4299	M	0.70275	2.135	0.80722	D	1	B;B;B;B;B;B	0.12630	0.002;0.001;0.002;0.006;0.006;0.002	B;B;B;B;B;B	0.10450	0.0;0.001;0.001;0.003;0.005;0.001	T	0.70781	-0.4779	10	0.30854	T	0.27	.	11.1164	0.48262	0.5039:0.0:0.4961:0.0	rs9895012	674;674;674;674;674;674	Q93084-4;Q93084-2;Q93084;Q93084-6;G3XAE1;Q93084-3	.;.;AT2A3_HUMAN;.;.;.	C	674	ENSP00000380236:R674C;ENSP00000301387:R674C;ENSP00000353072:R674C;ENSP00000380234:R674C;ENSP00000312577:R674C;ENSP00000380229:R674C	ENSP00000312577:R674C	R	-	1	0	ATP2A3	3791094	0.817000	0.29147	0.759000	0.31340	0.917000	0.54804	1.124000	0.31320	-0.821000	0.04312	-0.459000	0.05422	CGC		0.657	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
MYH3	4621	hgsc.bcm.edu	37	17	10542709	10542709	+	Missense_Mutation	SNP	G	G	A	rs34088014	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:10542709G>A	ENST00000583535.1	-	24	3095	c.3008C>T	c.(3007-3009)gCg>gTg	p.A1003V	MYH3_ENST00000226209.7_Missense_Mutation_p.A1003V	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	1003			A -> V (in dbSNP:rs34088014).		actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						CTGCTGGTGCGCCTCTTGGAG	0.443													G|||	109	0.0217652	0.0333	0.0086	5008	,	,		19720	0.003		0.0239	False		,,,				2504	0.0327																0			17						G	VAL/ALA	129,4277	93.9+/-132.6	2,125,2076	68.0	66.0	67.0		3008	5.5	1.0	17	dbSNP_126	67	177,8423	79.5+/-142.1	1,175,4124	yes	missense	MYH3	NM_002470.3	64	3,300,6200	AA,AG,GG		2.0581,2.9278,2.3528	benign	1003/1941	10542709	306,12700	2203	4300	6503	10483434	SO:0001583	missense	4621				CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"""Myosins / Myosin superfamily : Class II"""	7573	protein-coding gene	gene with protein product	"""myosin, skeletal, heavy chain, embryonic 1"", ""muscle embryonic myosin heavy chain 3"""	160720	"""myosin, heavy polypeptide 3, skeletal muscle, embryonic"""			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.3008C>T	17.37:g.10542709G>A	ENSP00000464317:p.Ala1003Val		10483434	Q15492	Missense_Mutation	SNP	ENST00000583535.1	37	CCDS11157.1	38	0.0173992673992674	14	0.028455284552845527	3	0.008287292817679558	1	0.0017482517482517483	20	0.026385224274406333	G	17.29	3.352176	0.61183	0.029278	0.020581	ENSG00000109063	ENST00000226209	D	0.83250	-1.7	5.54	5.54	0.83059	.	.	.	.	.	T	0.65709	0.2717	M	0.63843	1.955	0.54753	D	0.999988	B	0.15930	0.015	B	0.10450	0.005	T	0.72497	-0.4275	9	0.46703	T	0.11	.	19.8414	0.96690	0.0:0.0:1.0:0.0	rs34088014	1003	P11055	MYH3_HUMAN	V	1003	ENSP00000226209:A1003V	ENSP00000226209:A1003V	A	-	2	0	MYH3	10483434	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	6.734000	0.74801	2.763000	0.94921	0.650000	0.86243	GCG		0.443	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470	
NF1	4763	hgsc.bcm.edu	37	17	29528489	29528489	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:29528489C>T	ENST00000358273.4	+	11	1629	c.1246C>T	c.(1246-1248)Cga>Tga	p.R416*	NF1_ENST00000356175.3_Nonsense_Mutation_p.R416*|NF1_ENST00000431387.4_Nonsense_Mutation_p.R416*	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	416					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(6)|p.R416*(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TTCACTCCATCGAATCATCAC	0.308			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																													yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	15	Whole gene deletion(8)|Unknown(6)|Substitution - Nonsense(1)	soft_tissue(8)|autonomic_ganglia(3)|central_nervous_system(3)|lung(1)	17	GRCh37	CM992366	NF1	M							85.0	95.0	92.0					17																	29528489		2203	4294	6497	26552615	SO:0001587	stop_gained	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.1246C>T	17.37:g.29528489C>T	ENSP00000351015:p.Arg416*		26552615	O00662|Q14284|Q14930|Q14931|Q9UMK3	Nonsense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.751639	0.89753	.	.	ENSG00000196712	ENST00000431387;ENST00000358273;ENST00000356175;ENST00000456735	.	.	.	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.5894	0.61951	0.1554:0.8446:0.0:0.0	.	.	.	.	X	416;416;416;82	.	ENSP00000348498:R416X	R	+	1	2	NF1	26552615	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.539000	0.53604	2.408000	0.81797	0.484000	0.47621	CGA		0.308	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
ERBB2	2064	hgsc.bcm.edu	37	17	37882854	37882854	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:37882854A>G	ENST00000269571.5	+	24	3071	c.2912A>G	c.(2911-2913)gAg>gGg	p.E971G	ERBB2_ENST00000584601.1_Missense_Mutation_p.E941G|ERBB2_ENST00000406381.2_Missense_Mutation_p.E941G|ERBB2_ENST00000540147.1_Missense_Mutation_p.E941G|ERBB2_ENST00000584450.1_Missense_Mutation_p.E971G|ERBB2_ENST00000541774.1_Missense_Mutation_p.E956G|MIEN1_ENST00000474210.1_5'Flank|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000445658.2_Missense_Mutation_p.E695G			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	971	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.E971G(1)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	AGATTCCGGGAGTTGGTGTCT	0.612		1	"""A, Mis, O"""		"""breast, ovarian, other tumour types, NSCLC, gastric"""					TCGA GBM(5;<1E-08)																														Dom	yes		17	17q21.1	2064	"""v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"""		E	1	Substitution - Missense(1)	ovary(1)	17											132.0	107.0	116.0					17																	37882854		2203	4300	6503	35136380	SO:0001583	missense	2064			X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"""CD molecules"""	3430	protein-coding gene	gene with protein product	"""neuro/glioblastoma derived oncogene homolog"""	164870	"""v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"""	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.2912A>G	17.37:g.37882854A>G	ENSP00000269571:p.Glu971Gly		35136380	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	A	16.39	3.110891	0.56398	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24	5.29	5.29	0.74685	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.75568	0.3867	M	0.79011	2.435	0.80722	D	1	P;B;P	0.44309	0.832;0.108;0.832	P;B;P	0.49708	0.62;0.036;0.62	T	0.79706	-0.1691	9	0.87932	D	0	.	14.247	0.65995	1.0:0.0:0.0:0.0	.	695;956;971	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	G	941;956;695;971;941	ENSP00000385185:E941G;ENSP00000446466:E956G;ENSP00000404047:E695G;ENSP00000269571:E971G;ENSP00000443562:E941G	ENSP00000269571:E971G	E	+	2	0	ERBB2	35136380	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.523000	0.81856	2.003000	0.58678	0.533000	0.62120	GAG		0.612	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2		
EFCAB13	124989	hgsc.bcm.edu	37	17	45438838	45438838	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:45438838T>C	ENST00000331493.2	+	10	1167	c.756T>C	c.(754-756)ccT>ccC	p.P252P	EFCAB13_ENST00000517484.1_Intron	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	252						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										TGGGTATCCCTATAAACCGTG	0.353																																																	0			17											181.0	177.0	178.0					17																	45438838		2203	4300	6503	42793837	SO:0001819	synonymous_variant	124989			BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"""EF-hand domain containing"""	26864	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 57"""	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.756T>C	17.37:g.45438838T>C			42793837	G3V128|Q49AG9	Silent	SNP	ENST00000331493.2	37	CCDS11512.1																																																																																				0.353	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347	
LRRC59	55379	hgsc.bcm.edu	37	17	48462526	48462526	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:48462526T>C	ENST00000225972.7	-	6	864	c.629A>G	c.(628-630)aAg>aGg	p.K210R	Y_RNA_ENST00000384097.1_RNA	NM_018509.3	NP_060979.2	Q96AG4	LRC59_HUMAN	leucine rich repeat containing 59	210						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			CTGCTCCCGCTTGGCTGCTTT	0.552																																																	0			17											182.0	177.0	178.0					17																	48462526		2203	4300	6503	45817525	SO:0001583	missense	55379			AK025328	CCDS11566.1	17q21.33	2014-02-12	2006-01-12		ENSG00000108829	ENSG00000108829			28817	protein-coding gene	gene with protein product		614854				12477932	Standard	NM_018509		Approved	PRO1855, FLJ21675	uc002iqt.3	Q96AG4	OTTHUMG00000162079	ENST00000225972.7:c.629A>G	17.37:g.48462526T>C	ENSP00000225972:p.Lys210Arg		45817525	B2RE83|D3DTX8|Q9P189	Missense_Mutation	SNP	ENST00000225972.7	37	CCDS11566.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.775526	0.90195	.	.	ENSG00000108829	ENST00000225972	T	0.05199	3.48	5.87	5.87	0.94306	.	0.098404	0.64402	D	0.000001	T	0.12135	0.0295	L	0.53249	1.67	0.80722	D	1	P	0.51057	0.941	P	0.46917	0.531	T	0.02156	-1.1204	10	0.37606	T	0.19	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	210	Q96AG4	LRC59_HUMAN	R	210	ENSP00000225972:K210R	ENSP00000225972:K210R	K	-	2	0	LRRC59	45817525	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	2.976000	0.49289	2.371000	0.80710	0.533000	0.62120	AAG		0.552	LRRC59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367117.2	NM_018509	
MSI2	124540	hgsc.bcm.edu	37	17	55478755	55478755	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:55478755A>G	ENST00000284073.2	+	6	537	c.328A>G	c.(328-330)Aag>Gag	p.K110E	MSI2_ENST00000416426.2_Missense_Mutation_p.K88E|MSI2_ENST00000579180.1_Missense_Mutation_p.K6E|MSI2_ENST00000322684.3_Missense_Mutation_p.K106E|MSI2_ENST00000442934.2_Missense_Mutation_p.K49E	NM_138962.2	NP_620412.1	Q96DH6	MSI2H_HUMAN	musashi RNA-binding protein 2	110	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.|RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.					cytoplasm (GO:0005737)|polysome (GO:0005844)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(1)|pancreas(1)|skin(1)	7	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)		CACAAGAACAAAGAAAATATT	0.448			T	HOXA9	CML																																			Dom	yes		17	17q23.2	124540	musashi homolog 2 (Drosophila)		L	0			17											110.0	106.0	107.0					17																	55478755		2203	4300	6503	52833754	SO:0001583	missense	124540			BC001526	CCDS11596.1, CCDS11597.1	17q23.2	2013-07-16	2012-12-13					"""RNA binding motif (RRM) containing"""	18585	protein-coding gene	gene with protein product		607897	"""musashi homolog 2 (Drosophila)"""			11588182	Standard	NM_138962		Approved		uc002iuz.1	Q96DH6		ENST00000284073.2:c.328A>G	17.37:g.55478755A>G	ENSP00000284073:p.Lys110Glu		52833754	Q7Z6M7|Q8N9T4	Missense_Mutation	SNP	ENST00000284073.2	37	CCDS11596.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.823027	0.90873	.	.	ENSG00000153944	ENST00000416426;ENST00000284073;ENST00000322684;ENST00000442934	D;D;D;D	0.92858	-3.12;-3.12;-3.12;-3.12	5.5	5.5	0.81552	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.64402	D	0.000001	D	0.93785	0.8013	L	0.39898	1.24	0.54753	D	0.999988	D;D;D	0.58268	0.982;0.964;0.97	D;P;P	0.67548	0.952;0.889;0.777	D	0.94583	0.7781	10	0.87932	D	0	.	15.9002	0.79369	1.0:0.0:0.0:0.0	.	88;106;110	B4DHE8;Q96DH6-2;Q96DH6	.;.;MSI2H_HUMAN	E	88;110;106;49	ENSP00000414671:K88E;ENSP00000284073:K110E;ENSP00000313616:K106E;ENSP00000392607:K49E	ENSP00000284073:K110E	K	+	1	0	MSI2	52833754	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.867000	0.92314	2.219000	0.72066	0.533000	0.62120	AAG		0.448	MSI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441813.1		
MAP3K3	4215	hgsc.bcm.edu	37	17	61771046	61771046	+	Missense_Mutation	SNP	G	G	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:61771046G>T	ENST00000361733.3	+	16	2110	c.1790G>T	c.(1789-1791)cGg>cTg	p.R597L	MAP3K3_ENST00000579585.1_Missense_Mutation_p.R628L|MAP3K3_ENST00000361357.3_Missense_Mutation_p.R628L|MAP3K3_ENST00000584573.1_Missense_Mutation_p.R624L|MAP3K3_ENST00000577395.1_Missense_Mutation_p.R593L	NM_002401.3	NP_002392.2	Q99759	M3K3_HUMAN	mitogen-activated protein kinase kinase kinase 3	597	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein autophosphorylation (GO:0046777)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)	p.R597Q(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	28						GAACATGGCCGGGACTTCCTG	0.567																																																	1	Substitution - Missense(1)	large_intestine(1)	17											107.0	96.0	100.0					17																	61771046		2203	4300	6503	59124778	SO:0001583	missense	4215			U78876	CCDS32701.1, CCDS32702.1	17q	2011-06-09				ENSG00000198909		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6855	protein-coding gene	gene with protein product	"""MAP/ERK kinase kinase 3"", ""MAPK/ERK kinase kinase 3"""	602539		MEKK3		9006902	Standard	NM_002401		Approved	MAPKKK3	uc002jbf.3	Q99759		ENST00000361733.3:c.1790G>T	17.37:g.61771046G>T	ENSP00000354485:p.Arg597Leu		59124778	B2RCW2|D3DU15|Q5BKZ6|Q8N3I9	Missense_Mutation	SNP	ENST00000361733.3	37	CCDS32702.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.220934	0.79464	.	.	ENSG00000198909	ENST00000361357;ENST00000361733	T;T	0.64618	-0.11;-0.11	4.95	3.98	0.46160	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.73265	0.3565	L	0.57536	1.79	0.80722	D	1	D;D;P;B	0.61697	0.99;0.979;0.621;0.386	D;P;P;B	0.65010	0.931;0.879;0.527;0.392	T	0.76088	-0.3087	10	0.87932	D	0	.	13.4432	0.61125	0.0765:0.0:0.9235:0.0	.	593;565;597;628	Q1PBM3;Q96HN9;Q99759;Q99759-2	.;.;M3K3_HUMAN;.	L	628;597	ENSP00000354927:R628L;ENSP00000354485:R597L	ENSP00000354927:R628L	R	+	2	0	MAP3K3	59124778	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.835000	0.99442	1.085000	0.41206	0.561000	0.74099	CGG		0.567	MAP3K3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000443867.1	NM_002401	
ABCA6	23460	hgsc.bcm.edu	37	17	67079367	67079367	+	Silent	SNP	C	C	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:67079367C>A	ENST00000284425.2	-	35	4635	c.4461G>T	c.(4459-4461)gtG>gtT	p.V1487V	ABCA6_ENST00000446604.2_5'UTR	NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	1487	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					GCCTTCCAGACACCATGATGG	0.532																																																	0			17											100.0	84.0	90.0					17																	67079367		2203	4300	6503	64590962	SO:0001819	synonymous_variant	23460			U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"""ATP binding cassette transporters / subfamily A"""	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.4461G>T	17.37:g.67079367C>A			64590962	Q6NSH9|Q8N856|Q8WWZ6	Silent	SNP	ENST00000284425.2	37	CCDS11683.1																																																																																				0.532	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284	
ABCA10	10349	hgsc.bcm.edu	37	17	67153002	67153002	+	Missense_Mutation	SNP	A	A	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:67153002A>T	ENST00000269081.4	-	29	4335	c.3426T>A	c.(3424-3426)aaT>aaA	p.N1142K	ABCA10_ENST00000416101.2_3'UTR|ABCA10_ENST00000519732.1_5'UTR	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	1142					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					TCATTATTTCATTTCCATACT	0.264																																																	0			17											27.0	27.0	27.0					17																	67153002		2200	4294	6494	64664597	SO:0001583	missense	10349			AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"""ATP binding cassette transporters / subfamily A"""	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.3426T>A	17.37:g.67153002A>T	ENSP00000269081:p.Asn1142Lys		64664597	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Missense_Mutation	SNP	ENST00000269081.4	37	CCDS11684.1	.	.	.	.	.	.	.	.	.	.	A	0.298	-0.975616	0.02215	.	.	ENSG00000154263	ENST00000269081	D	0.86366	-2.11	3.28	-5.12	0.02893	.	0.766269	0.10439	N	0.674483	T	0.44180	0.1281	N	0.00125	-2.05	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.59434	-0.7455	10	0.02654	T	1	.	2.9049	0.05718	0.1618:0.4537:0.1056:0.2789	.	134;1142	B4DPV2;Q8WWZ4	.;ABCAA_HUMAN	K	1142	ENSP00000269081:N1142K	ENSP00000269081:N1142K	N	-	3	2	ABCA10	64664597	0.000000	0.05858	0.019000	0.16419	0.992000	0.81027	-2.458000	0.01000	-0.692000	0.05128	0.460000	0.39030	AAT		0.264	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282	
PRPSAP1	5635	hgsc.bcm.edu	37	17	74309925	74309925	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:74309925C>T	ENST00000446526.3	-	8	1274	c.829G>A	c.(829-831)Gga>Aga	p.G277R	PRPSAP1_ENST00000588364.1_5'Flank|PRPSAP1_ENST00000324684.4_Missense_Mutation_p.G174R	NM_002766.2	NP_002757.2	Q14558	KPRA_HUMAN	phosphoribosyl pyrophosphate synthetase-associated protein 1	248					negative regulation of kinase activity (GO:0033673)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide biosynthetic process (GO:0009165)	ribose phosphate diphosphokinase complex (GO:0002189)	enzyme inhibitor activity (GO:0004857)|magnesium ion binding (GO:0000287)|ribose phosphate diphosphokinase activity (GO:0004749)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	17						ATGCGGCCTCCAACATCTCCA	0.458																																																	0			17											208.0	159.0	176.0					17																	74309925		2203	4300	6503	71821520	SO:0001583	missense	5635			D61391	CCDS11743.2	17q24-q25	2008-07-18			ENSG00000161542	ENSG00000161542			9466	protein-coding gene	gene with protein product		601249				8660991	Standard	NM_002766		Approved	PAP39	uc010wta.1	Q14558	OTTHUMG00000155969	ENST00000446526.3:c.829G>A	17.37:g.74309925C>T	ENSP00000414624:p.Gly277Arg		71821520	B2R6M4|Q96H06	Missense_Mutation	SNP	ENST00000446526.3	37	CCDS11743.2	.	.	.	.	.	.	.	.	.	.	C	19.42	3.825063	0.71143	.	.	ENSG00000161542	ENST00000446526;ENST00000324684;ENST00000435555	T;T;T	0.73681	-0.77;-0.77;-0.77	5.81	5.81	0.92471	.	0.106285	0.64402	D	0.000004	T	0.72882	0.3516	N	0.25789	0.76	0.80722	D	1	P;B	0.51653	0.947;0.439	P;B	0.54270	0.747;0.249	T	0.69247	-0.5195	10	0.26408	T	0.33	.	15.5584	0.76219	0.0:0.8628:0.1372:0.0	.	248;277	Q14558;Q14558-2	KPRA_HUMAN;.	R	277;174;174	ENSP00000414624:G277R;ENSP00000314973:G174R;ENSP00000392838:G174R	ENSP00000314973:G174R	G	-	1	0	PRPSAP1	71821520	1.000000	0.71417	0.935000	0.37517	0.986000	0.74619	5.965000	0.70387	2.746000	0.94184	0.591000	0.81541	GGA		0.458	PRPSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342480.2	NM_002766	
RNF213	57674	hgsc.bcm.edu	37	17	78291028	78291028	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:78291028A>G	ENST00000582970.1	+	16	2995	c.2852A>G	c.(2851-2853)cAt>cGt	p.H951R	CTD-2047H16.2_ENST00000576808.1_RNA|RNF213_ENST00000319921.4_Missense_Mutation_p.H951R|RNF213_ENST00000456466.1_Missense_Mutation_p.H951R|RNF213_ENST00000508628.2_Missense_Mutation_p.H1000R	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	951					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CCCGCGGAGCATGGCTGGAAG	0.572																																																	0			17											88.0	82.0	84.0					17																	78291028		2203	4298	6501	75905623	SO:0001583	missense	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.2852A>G	17.37:g.78291028A>G	ENSP00000464087:p.His951Arg		75905623	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	a	6.305	0.424450	0.11928	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000456466;ENST00000319921	T;T	0.13538	2.58;2.58	3.71	-0.144	0.13440	.	1.326120	0.05384	N	0.537744	T	0.18676	0.0448	L	0.43152	1.355	0.09310	N	1	D;D	0.64830	0.962;0.994	P;P	0.54026	0.605;0.74	T	0.17776	-1.0358	10	0.38643	T	0.18	-7.7398	3.9507	0.09368	0.4237:0.1961:0.0:0.3802	.	951;951	Q9HCF4;Q9HCF4-2	ALO17_HUMAN;.	R	951;1000;951;951	ENSP00000392123:H951R;ENSP00000324392:H951R	ENSP00000324392:H951R	H	+	2	0	RNF213	75905623	0.000000	0.05858	0.000000	0.03702	0.725000	0.41563	-0.165000	0.09968	-0.056000	0.13221	0.525000	0.51046	CAT		0.572	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
APP	351	hgsc.bcm.edu	37	21	27484438	27484438	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr21:27484438A>G	ENST00000346798.3	-	2	116	c.83T>C	c.(82-84)cTg>cCg	p.L28P	APP_ENST00000348990.5_Missense_Mutation_p.L28P|APP_ENST00000358918.3_Missense_Mutation_p.L28P|APP_ENST00000354192.3_Intron|APP_ENST00000359726.3_Missense_Mutation_p.L28P|APP_ENST00000357903.3_Missense_Mutation_p.L28P|APP_ENST00000474136.1_5'UTR|APP_ENST00000448388.2_5'UTR|APP_ENST00000440126.3_Missense_Mutation_p.L23P|APP_ENST00000439274.2_Intron	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	28					adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				TTCAGCCAGCAGGCCAGCATT	0.488																																																	0			21											119.0	106.0	111.0					21																	27484438		2203	4300	6503	26406309	SO:0001583	missense	351			M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"""Endogenous ligands"""	620	protein-coding gene	gene with protein product	"""peptidase nexin-II"""	104760	"""Alzheimer disease"""	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.83T>C	21.37:g.27484438A>G	ENSP00000284981:p.Leu28Pro		26406309	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Missense_Mutation	SNP	ENST00000346798.3	37	CCDS13576.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.318766	0.81469	.	.	ENSG00000142192	ENST00000346798;ENST00000348990;ENST00000357903;ENST00000358918;ENST00000359726;ENST00000440126	D;D;D;D;D;D	0.96427	-2.05;-4.01;-2.07;-1.91;-4.01;-2.09	5.44	5.44	0.79542	Amyloidogenic glycoprotein, heparin-binding (1);Amyloidogenic glycoprotein, extracellular (1);	0.000000	0.64402	D	0.000001	D	0.97476	0.9174	M	0.61703	1.905	0.80722	D	1	D;B;D;D;D	0.89917	1.0;0.111;0.999;0.996;0.998	D;B;D;D;D	0.91635	0.999;0.086;0.985;0.968;0.988	D	0.97603	1.0124	10	0.46703	T	0.11	-15.0248	15.1534	0.72720	1.0:0.0:0.0:0.0	.	28;23;28;28;28	P05067-2;B4DII8;P05067-4;P05067-8;P05067	.;.;.;.;A4_HUMAN	P	28;28;28;28;28;23	ENSP00000284981:L28P;ENSP00000345463:L28P;ENSP00000350578:L28P;ENSP00000351796:L28P;ENSP00000352760:L28P;ENSP00000387483:L23P	ENSP00000284981:L28P	L	-	2	0	APP	26406309	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.051000	0.76627	2.047000	0.60756	0.533000	0.62120	CTG		0.488	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484	
SLC5A3	6526	hgsc.bcm.edu	37	21	35469094	35469094	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr21:35469094A>G	ENST00000381151.3	+	2	2109	c.1597A>G	c.(1597-1599)Aca>Gca	p.T533A	SLC5A3_ENST00000608209.1_Missense_Mutation_p.T533A|AP000320.7_ENST00000362077.4_RNA|MRPS6_ENST00000399312.2_Intron			P53794	SC5A3_HUMAN	solute carrier family 5 (sodium/myo-inositol cotransporter), member 3	533					inositol metabolic process (GO:0006020)|peripheral nervous system development (GO:0007422)|regulation of respiratory gaseous exchange (GO:0043576)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	myo-inositol:sodium symporter activity (GO:0005367)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	20						GAGCCTTCTCACACCACCTCC	0.468																																																	0			21											80.0	69.0	73.0					21																	35469094		2203	4300	6503	34390964	SO:0001583	missense	6526				CCDS33549.1	21q22.11	2013-05-22	2008-09-02		ENSG00000198743	ENSG00000198743		"""Solute carriers"""	11038	protein-coding gene	gene with protein product		600444	"""solute carrier family 5 (inositol transporter), member 3"""			7789985	Standard	NM_006933		Approved	SMIT, SMIT1	uc002yto.3	P53794	OTTHUMG00000065821	ENST00000381151.3:c.1597A>G	21.37:g.35469094A>G	ENSP00000370543:p.Thr533Ala		34390964	O43489	Missense_Mutation	SNP	ENST00000381151.3	37	CCDS33549.1	.	.	.	.	.	.	.	.	.	.	A	17.44	3.389658	0.61956	.	.	ENSG00000198743	ENST00000381151	T	0.66280	-0.2	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.74688	0.3749	M	0.80422	2.495	0.48696	D	0.999697	D	0.54772	0.968	P	0.53401	0.725	T	0.79317	-0.1853	10	0.87932	D	0	.	15.1328	0.72539	1.0:0.0:0.0:0.0	.	533	P53794	SC5A3_HUMAN	A	533	ENSP00000370543:T533A	ENSP00000370543:T533A	T	+	1	0	SLC5A3	34390964	1.000000	0.71417	0.993000	0.49108	0.958000	0.62258	8.930000	0.92872	2.224000	0.72417	0.533000	0.62120	ACA		0.468	SLC5A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000141037.1		
COL18A1	80781	hgsc.bcm.edu	37	21	46875779	46875779	+	Missense_Mutation	SNP	C	C	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr21:46875779C>A	ENST00000359759.4	+	1	356	c.335C>A	c.(334-336)gCc>gAc	p.A112D	COL18A1_ENST00000355480.5_Missense_Mutation_p.A112D|COL18A1_ENST00000400337.2_Intron			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	112					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GGTGTCGGAGCCGAGATCCTG	0.637																																																	0			21											39.0	48.0	45.0					21																	46875779		2159	4258	6417	45700207	SO:0001583	missense	80781				CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.335C>A	21.37:g.46875779C>A	ENSP00000352798:p.Ala112Asp		45700207	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		.	.	.	.	.	.	.	.	.	.	C	10.38	1.335038	0.24253	.	.	ENSG00000182871	ENST00000355480;ENST00000359759;ENST00000539645	T;T	0.53206	0.63;0.63	3.68	3.68	0.42216	Domain of unknown function DUF959, collagen XVIII, N-terminal (1);	0.274745	0.22560	N	0.058479	T	0.65123	0.2661	M	0.66939	2.045	0.33684	D	0.612495	D;D	0.69078	0.997;0.996	D;D	0.70935	0.971;0.951	T	0.77294	-0.2641	10	0.87932	D	0	.	14.3285	0.66537	0.0:1.0:0.0:0.0	.	112;112	P39060;P39060-1	COIA1_HUMAN;.	D	112	ENSP00000347665:A112D;ENSP00000352798:A112D	ENSP00000347665:A112D	A	+	2	0	COL18A1	45700207	0.583000	0.26757	0.989000	0.46669	0.092000	0.18411	0.017000	0.13399	1.781000	0.52344	0.313000	0.20887	GCC		0.637	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
COL6A2	1292	hgsc.bcm.edu	37	21	47552085	47552085	+	Silent	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr21:47552085G>A	ENST00000300527.4	+	28	2783	c.2679G>A	c.(2677-2679)ccG>ccA	p.P893P		NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	893	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		TGGCCTTCCCGCTGAGCCACA	0.682																																																	0			21																																								46376513	SO:0001819	synonymous_variant	1292			M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2679G>A	21.37:g.47552085G>A			46376513	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Silent	SNP	ENST00000300527.4	37	CCDS13728.1																																																																																				0.682	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
TPSD1	23430	hgsc.bcm.edu	37	16	1306355	1306355	+	Missense_Mutation	SNP	T	T	C	rs1800984	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr16:1306355T>C	ENST00000211076.3	+	1	222	c.74T>C	c.(73-75)gTg>gCg	p.V25A	TPSD1_ENST00000397534.2_Missense_Mutation_p.V18A|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	25			V -> A (in dbSNP:rs1800984).	V -> G (in Ref. 1; AAD17861). {ECO:0000305}.		extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				CCGGCCTACGTGGCCCCTGGT	0.721													-|||	3599	0.71865	0.7564	0.6542	5008	,	,		14753	0.9484		0.5577	False		,,,				2504	0.6421																0			16						T	ALA/VAL	3121,1271		1094,933,169	29.0	37.0	34.0		74	-3.1	0.0	16	dbSNP_89	34	4690,3906		1125,2440,733	no	missense	TPSD1	NM_012217.2	64	2219,3373,902	CC,CT,TT		45.4397,28.939,39.8599	benign	25/243	1306355	7811,5177	2196	4298	6494	1246356	SO:0001583	missense	23430			AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.74T>C	16.37:g.1306355T>C	ENSP00000211076:p.Val25Ala		1246356	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	1558	0.7133699633699634	388	0.7886178861788617	208	0.574585635359116	556	0.972027972027972	406	0.5356200527704486	-	0.855	-0.737258	0.03111	0.71061	0.545603	ENSG00000095917	ENST00000397534;ENST00000211076	T;T	0.81247	-1.47;-1.47	2.55	-3.13	0.05266	.	0.813971	0.10635	N	0.651704	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35076	-0.9803	9	0.02654	T	1	.	3.4489	0.07491	0.0:0.375:0.2043:0.4206	rs1800984;rs3865206;rs4083416	25	Q9BZJ3	TRYD_HUMAN	A	18;25	ENSP00000380668:V18A;ENSP00000211076:V25A	ENSP00000211076:V25A	V	+	2	0	TPSD1	1246356	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.814000	0.01723	-0.826000	0.04284	-1.137000	0.01932	GTG		0.721	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
EME2	197342	hgsc.bcm.edu	37	16	1823754	1823754	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr16:1823754C>T	ENST00000568449.1	+	2	317	c.296C>T	c.(295-297)gCc>gTc	p.A99V	MRPS34_ENST00000397375.2_5'Flank|EME2_ENST00000307394.7_Missense_Mutation_p.A99V|NME3_ENST00000219302.3_5'Flank|MRPS34_ENST00000177742.3_5'Flank|NME3_ENST00000563498.1_5'Flank	NM_001257370.1	NP_001244299.1	A4GXA9	EME2_HUMAN	essential meiotic structure-specific endonuclease subunit 2	99					DNA recombination (GO:0006310)|DNA repair (GO:0006281)	nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)			central_nervous_system(1)|kidney(2)|lung(5)|pancreas(1)	9						GCCCTGGAGGCCCTGGGCTGC	0.741								Direct reversal of damage;Homologous recombination																																									0			16											5.0	4.0	4.0					16																	1823754		1791	3575	5366	1763755	SO:0001583	missense	197342			AK074080	CCDS58404.1	16p13.3	2013-07-03	2013-07-03			ENSG00000197774			27289	protein-coding gene	gene with protein product	"""SLX2 structure-specific endonuclease subunit homolog B (S. cerevisiae)"""	610886	"""essential meiotic endonuclease 1 homolog 2 (S. pombe)"""			12721304	Standard	NM_001257370		Approved	FLJ00151, SLX2B	uc010brw.1	A4GXA9		ENST00000568449.1:c.296C>T	16.37:g.1823754C>T	ENSP00000457353:p.Ala99Val		1763755	Q8TEP2|Q96RY3	Missense_Mutation	SNP	ENST00000568449.1	37	CCDS58404.1	.	.	.	.	.	.	.	.	.	.	C	10.09	1.255434	0.22965	.	.	ENSG00000197774	ENST00000307394;ENST00000454910	T	0.23147	1.92	3.56	2.57	0.30868	ERCC4 domain (2);	1.209980	0.06420	U	0.722101	T	0.16599	0.0399	.	.	.	0.09310	N	1	B	0.25850	0.136	B	0.24701	0.055	T	0.19549	-1.0302	9	0.29301	T	0.29	-1.3381	6.4619	0.21960	0.0:0.7682:0.0:0.2318	.	99	A4GXA9	EME2_HUMAN	V	99	ENSP00000303779:A99V	ENSP00000303779:A99V	A	+	2	0	EME2	1763755	0.001000	0.12720	0.231000	0.23993	0.792000	0.44763	1.611000	0.36879	1.707000	0.51288	0.306000	0.20318	GCC		0.741	EME2-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433185.2	NM_001010865	
GTF3C1	2975	hgsc.bcm.edu	37	16	27512525	27512525	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr16:27512525C>T	ENST00000356183.4	-	12	2063	c.2048G>A	c.(2047-2049)gGc>gAc	p.G683D	GTF3C1_ENST00000561623.1_Missense_Mutation_p.G683D	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	683					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						CTTCTTGATGCCATCTTGAAT	0.527																																																	0			16											128.0	103.0	111.0					16																	27512525		2197	4300	6497	27420026	SO:0001583	missense	2975			U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.2048G>A	16.37:g.27512525C>T	ENSP00000348510:p.Gly683Asp		27420026	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	37	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.880473	0.91740	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.24908	1.83	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.51686	0.1689	M	0.67953	2.075	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.47971	-0.9075	10	0.51188	T	0.08	-13.1534	19.0541	0.93056	0.0:1.0:0.0:0.0	.	683;683	Q12789;Q12789-3	TF3C1_HUMAN;.	D	683;681	ENSP00000348510:G683D	ENSP00000348510:G683D	G	-	2	0	GTF3C1	27420026	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	7.256000	0.78350	2.655000	0.90218	0.655000	0.94253	GGC		0.527	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	
CYLD	1540	hgsc.bcm.edu	37	16	50811825	50811825	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr16:50811825T>C	ENST00000427738.3	+	7	1316	c.1111T>C	c.(1111-1113)Tca>Cca	p.S371P	CYLD_ENST00000564326.1_Missense_Mutation_p.S368P|CYLD_ENST00000568704.2_Missense_Mutation_p.S368P|CYLD_ENST00000540145.1_Missense_Mutation_p.S371P|CYLD_ENST00000311559.9_Missense_Mutation_p.S371P|CYLD_ENST00000566206.1_Missense_Mutation_p.S368P|CYLD_ENST00000398568.2_Missense_Mutation_p.S368P|CYLD_ENST00000569418.1_Missense_Mutation_p.S368P			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	371	Interaction with TRIP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				ACAATCCAAATCAAAAAATAC	0.313			"""Mis, N, F, S"""		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																														yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	0			16											87.0	81.0	83.0					16																	50811825		1814	4061	5875	49369326	SO:0001583	missense	1540	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"""ubiquitin specific peptidase like 2"""	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.1111T>C	16.37:g.50811825T>C	ENSP00000392025:p.Ser371Pro		49369326	O94934|Q7L3N6|Q96EH0|Q9NZX9	Missense_Mutation	SNP	ENST00000427738.3	37	CCDS45482.1	.	.	.	.	.	.	.	.	.	.	T	13.56	2.272448	0.40194	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	D;D;D	0.93906	-3.31;-3.31;-3.31	5.57	3.25	0.37280	.	0.283087	0.35870	N	0.002940	D	0.85327	0.5671	N	0.24115	0.695	0.42188	D	0.991711	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.09377	0.0;0.004;0.0;0.0	T	0.77953	-0.2394	10	0.35671	T	0.21	-6.4529	6.1147	0.20120	0.2678:0.072:0.0:0.6602	.	368;371;368;371	A8KAB0;F5H2R7;Q9NQC7-2;Q9NQC7	.;.;.;CYLD_HUMAN	P	371;371;368;368	ENSP00000445447:S371P;ENSP00000308928:S371P;ENSP00000381574:S368P	ENSP00000308928:S371P	S	+	1	0	CYLD	49369326	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.942000	0.40243	0.995000	0.38917	0.528000	0.53228	TCA		0.313	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2		
CHD9	80205	hgsc.bcm.edu	37	16	53272297	53272297	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr16:53272297T>C	ENST00000398510.3	+	11	2763	c.2676T>C	c.(2674-2676)acT>acC	p.T892T	CHD9_ENST00000564845.1_Silent_p.T892T|CHD9_ENST00000447540.1_Silent_p.T892T|CHD9_ENST00000566029.1_Silent_p.T892T			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	892	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.T892T(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				TTGGCAAAACTATTCAATCAA	0.348																																																	1	Substitution - coding silent(1)	kidney(1)	16											91.0	85.0	87.0					16																	53272297		1831	4084	5915	51829798	SO:0001819	synonymous_variant	80205			AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.2676T>C	16.37:g.53272297T>C			51829798	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Silent	SNP	ENST00000398510.3	37																																																																																					0.348	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134	
WWP2	11060	hgsc.bcm.edu	37	16	69971053	69971053	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr16:69971053T>C	ENST00000359154.2	+	20	2251	c.2150T>C	c.(2149-2151)gTg>gCg	p.V717A	WWP2_ENST00000568684.1_Missense_Mutation_p.V278A|WWP2_ENST00000448661.1_Missense_Mutation_p.V717A|WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000542271.1_Missense_Mutation_p.V601A|WWP2_ENST00000356003.2_Missense_Mutation_p.V717A	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	717	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cellular protein modification process (GO:0006464)|negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transporter activity (GO:0032410)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)			breast(4)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						ACCCGAGGCGTGGAAGAGCAG	0.617																																																	0			16											77.0	68.0	71.0					16																	69971053		2198	4300	6498	68528554	SO:0001583	missense	11060			BC013645	CCDS10885.1, CCDS58475.1, CCDS58476.1, CCDS58477.1	16q22.1	2008-02-05			ENSG00000198373	ENSG00000198373			16804	protein-coding gene	gene with protein product		602308				9169421, 12167593	Standard	NM_007014		Approved	AIP2	uc002exv.2	O00308	OTTHUMG00000137573	ENST00000359154.2:c.2150T>C	16.37:g.69971053T>C	ENSP00000352069:p.Val717Ala		68528554	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Missense_Mutation	SNP	ENST00000359154.2	37	CCDS10885.1	.	.	.	.	.	.	.	.	.	.	T	31	5.065869	0.93898	.	.	ENSG00000198373	ENST00000359154;ENST00000545099;ENST00000448661;ENST00000356003;ENST00000544162;ENST00000542271	T;T;T;T	0.62232	0.04;0.04;0.04;0.04	5.21	5.21	0.72293	HECT (4);	0.000000	0.85682	D	0.000000	T	0.81365	0.4807	M	0.87180	2.865	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	D	0.84442	0.0583	9	.	.	.	.	15.3883	0.74723	0.0:0.0:0.0:1.0	.	717	O00308	WWP2_HUMAN	A	717;278;717;717;604;601	ENSP00000352069:V717A;ENSP00000396871:V717A;ENSP00000348283:V717A;ENSP00000445616:V601A	.	V	+	2	0	WWP2	68528554	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	7.997000	0.88414	2.077000	0.62373	0.533000	0.62120	GTG		0.617	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014	
CDYL2	124359	hgsc.bcm.edu	37	16	80638362	80638362	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr16:80638362G>A	ENST00000570137.2	-	7	1599	c.1444C>T	c.(1444-1446)Ctc>Ttc	p.L482F	CDYL2_ENST00000562812.1_Missense_Mutation_p.L483F|CDYL2_ENST00000563890.1_Missense_Mutation_p.L483F|CDYL2_ENST00000566173.1_Missense_Mutation_p.L483F	NM_152342.2	NP_689555.2	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2	482						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	21						AGCTGCTTGAGCATGAGGCAT	0.542																																																	0			16											135.0	129.0	131.0					16																	80638362		2203	4300	6503	79195863	SO:0001583	missense	124359			AK096185	CCDS32493.1	16q23.2	2008-02-05	2003-09-12			ENSG00000166446			23030	protein-coding gene	gene with protein product			"""chromodomain Y-like protein 2"""			12837688	Standard	NM_152342		Approved	FLJ38866	uc002ffs.3	Q8N8U2		ENST00000570137.2:c.1444C>T	16.37:g.80638362G>A	ENSP00000476295:p.Leu482Phe		79195863	Q7Z5I8	Missense_Mutation	SNP	ENST00000570137.2	37	CCDS32493.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.167966	0.78339	.	.	ENSG00000166446	ENST00000299564	T	0.65364	-0.15	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000002	T	0.81692	0.4876	M	0.91140	3.18	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	D	0.84662	0.0707	10	0.87932	D	0	.	11.0713	0.48006	0.0923:0.0:0.9077:0.0	.	482	Q8N8U2	CDYL2_HUMAN	F	482	ENSP00000299564:L482F	ENSP00000299564:L482F	L	-	1	0	CDYL2	79195863	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.966000	0.40481	2.717000	0.92951	0.650000	0.86243	CTC		0.542	CDYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434727.2	NM_152342	
TLDC1	57707	hgsc.bcm.edu	37	16	84522896	84522896	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr16:84522896T>C	ENST00000343629.6	-	4	699	c.517A>G	c.(517-519)Atg>Gtg	p.M173V	TLDC1_ENST00000561807.1_5'Flank|TLDC1_ENST00000535580.1_Missense_Mutation_p.M146V	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	173						lysosomal membrane (GO:0005765)											TGCAGCTTCATGTCAGAGAGC	0.582																																																	0			16											50.0	47.0	48.0					16																	84522896		2200	4300	6500	83080397	SO:0001583	missense	57707			AB046829	CCDS32498.1	16q24.1	2013-03-14	2013-03-14	2013-03-14	ENSG00000140950	ENSG00000140950			29325	protein-coding gene	gene with protein product	"""TLD domain containing 1"""		"""KIAA1609"""	KIAA1609		10997877	Standard	NM_020947		Approved		uc002fib.3	Q6P9B6	OTTHUMG00000176739	ENST00000343629.6:c.517A>G	16.37:g.84522896T>C	ENSP00000343635:p.Met173Val		83080397	Q8IZ64|Q9HCG3|Q9NTE8	Missense_Mutation	SNP	ENST00000343629.6	37	CCDS32498.1	.	.	.	.	.	.	.	.	.	.	t	11.55	1.672637	0.29693	.	.	ENSG00000140950	ENST00000343629;ENST00000535580	T;T	0.09163	3.2;3.01	5.04	1.27	0.21489	.	0.465387	0.24879	N	0.034869	T	0.09335	0.0230	M	0.62723	1.935	0.23198	N	0.998133	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.28522	-1.0041	10	0.31617	T	0.26	-19.7902	2.5659	0.04783	0.1426:0.099:0.4438:0.3146	.	146;173	F5GWS3;Q6P9B6	.;K1609_HUMAN	V	173;146	ENSP00000343635:M173V;ENSP00000441997:M146V	ENSP00000343635:M173V	M	-	1	0	KIAA1609	83080397	0.412000	0.25392	0.992000	0.48379	0.784000	0.44337	-0.489000	0.06490	0.213000	0.20722	-0.332000	0.08345	ATG		0.582	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947	
MYOM1	8736	hgsc.bcm.edu	37	18	3188882	3188882	+	Missense_Mutation	SNP	C	C	T	rs200770047		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr18:3188882C>T	ENST00000356443.4	-	4	968	c.635G>A	c.(634-636)aGg>aAg	p.R212K	RP13-270P17.2_ENST00000580139.1_RNA|MYOM1_ENST00000400569.3_Missense_Mutation_p.R212K|MYOM1_ENST00000261606.7_Missense_Mutation_p.R212K	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	212	6 X 6 AA tandem repeats.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.R212K(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CGTGGACTGCCTGGATGCCGT	0.517																																																	1	Substitution - Missense(1)	endometrium(1)	18											260.0	242.0	248.0					18																	3188882		2044	4187	6231	3178882	SO:0001583	missense	8736			AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.635G>A	18.37:g.3188882C>T	ENSP00000348821:p.Arg212Lys		3178882	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	2.966	-0.213546	0.06140	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.45668	1.03;1.04;0.89	3.23	0.752	0.18398	.	0.084010	0.41097	N	0.000942	T	0.14830	0.0358	N	0.08118	0	0.09310	N	0.999995	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28808	-1.0032	10	0.05351	T	0.99	.	4.9448	0.13984	0.0:0.2653:0.0:0.7347	.	212;212	P52179-2;P52179	.;MYOM1_HUMAN	K	212	ENSP00000348821:R212K;ENSP00000383413:R212K;ENSP00000261606:R212K	ENSP00000261606:R212K	R	-	2	0	MYOM1	3178882	0.789000	0.28775	0.018000	0.16275	0.000000	0.00434	1.455000	0.35190	0.165000	0.19558	-1.097000	0.02148	AGG		0.517	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
DSC2	1824	hgsc.bcm.edu	37	18	28666673	28666673	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr18:28666673T>C	ENST00000280904.6	-	7	1251	c.808A>G	c.(808-810)Aaa>Gaa	p.K270E	DSC2_ENST00000251081.6_Missense_Mutation_p.K270E	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	270	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell-cardiac muscle cell adhesion (GO:0086042)|cell adhesion (GO:0007155)|cellular response to starvation (GO:0009267)|homophilic cell adhesion (GO:0007156)|regulation of heart rate by cardiac conduction (GO:0086091)|ventricular cardiac muscle cell action potential (GO:0086005)	cell-cell adherens junction (GO:0005913)|cytoplasmic vesicle (GO:0031410)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.K270*(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			GGCTCATCTTTGTCAGTAGCA	0.453																																																	1	Substitution - Nonsense(1)	ovary(1)	18											231.0	185.0	200.0					18																	28666673		2203	4300	6503	26920671	SO:0001583	missense	1825			X56807	CCDS11892.1, CCDS11893.1	18q12.1	2014-09-17			ENSG00000134755	ENSG00000134755		"""Cadherins / Major cadherins"""	3036	protein-coding gene	gene with protein product		125645		DSC3		7774948	Standard	NM_024422		Approved	CDHF2	uc002kwl.4	Q02487	OTTHUMG00000131981	ENST00000280904.6:c.808A>G	18.37:g.28666673T>C	ENSP00000280904:p.Lys270Glu		26920671		Missense_Mutation	SNP	ENST00000280904.6	37	CCDS11892.1	.	.	.	.	.	.	.	.	.	.	T	11.55	1.672223	0.29693	.	.	ENSG00000134755	ENST00000251081;ENST00000280904;ENST00000438199;ENST00000399347	T;T	0.61040	0.14;0.14	5.61	1.79	0.24919	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.50017	0.1591	L	0.38692	1.165	0.09310	N	0.999999	P;P	0.41848	0.763;0.721	P;B	0.46208	0.507;0.373	T	0.34527	-0.9825	9	0.41790	T	0.15	.	6.549	0.22423	0.0:0.0989:0.2884:0.6127	.	270;270	Q02487;Q02487-2	DSC2_HUMAN;.	E	270;270;36;283	ENSP00000251081:K270E;ENSP00000280904:K270E	ENSP00000251081:K270E	K	-	1	0	DSC2	26920671	0.857000	0.29778	0.871000	0.34182	0.275000	0.26752	1.198000	0.32223	0.370000	0.24538	0.533000	0.62120	AAA		0.453	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949	
DSG2	1829	hgsc.bcm.edu	37	18	29111211	29111211	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr18:29111211G>A	ENST00000261590.8	+	9	1485	c.1276G>A	c.(1276-1278)Gca>Aca	p.A426T		NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2	426	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|regulation of heart rate by cardiac conduction (GO:0086091)|response to progesterone (GO:0032570)|ventricular cardiac muscle cell action potential (GO:0086005)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(2)|prostate(4)|skin(2)|urinary_tract(1)	49			OV - Ovarian serous cystadenocarcinoma(10;0.0068)			ACCAGCCCATGCAAGGTAAGA	0.348																																																	0			18											102.0	92.0	95.0					18																	29111211		1859	4095	5954	27365209	SO:0001583	missense	1829			Z26317	CCDS42423.1	18q12.1	2014-09-17				ENSG00000046604		"""Cadherins / Major cadherins"""	3049	protein-coding gene	gene with protein product		125671				1612610	Standard	NM_001943		Approved	CDHF5	uc002kwu.4	Q14126		ENST00000261590.8:c.1276G>A	18.37:g.29111211G>A	ENSP00000261590:p.Ala426Thr		27365209	Q4KKU6	Missense_Mutation	SNP	ENST00000261590.8	37	CCDS42423.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.651336	0.47362	.	.	ENSG00000046604	ENST00000261590	T	0.54279	0.58	5.02	5.02	0.67125	Cadherin (4);Cadherin-like (1);	0.374516	0.22696	N	0.056741	T	0.30885	0.0779	N	0.03608	-0.345	0.58432	D	0.999999	P	0.39717	0.684	B	0.38378	0.272	T	0.38650	-0.9651	10	0.87932	D	0	.	12.3349	0.55060	0.0879:0.0:0.9121:0.0	.	426	Q14126	DSG2_HUMAN	T	426	ENSP00000261590:A426T	ENSP00000261590:A426T	A	+	1	0	DSG2	27365209	0.411000	0.25384	0.283000	0.24790	0.009000	0.06853	3.061000	0.49963	2.606000	0.88127	0.491000	0.48974	GCA		0.348	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	NM_001943	
SMAD4	4089	hgsc.bcm.edu	37	18	48603020	48603020	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr18:48603020C>T	ENST00000342988.3	+	11	1859	c.1321C>T	c.(1321-1323)Cgt>Tgt	p.R441C	SMAD4_ENST00000588745.1_Missense_Mutation_p.R345C|SMAD4_ENST00000398417.2_Missense_Mutation_p.R441C	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	441	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)|p.R441fs*16(1)|p.R441C(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		CTTTGATTTGCGTCAGTGTCA	0.448																																																	40	Whole gene deletion(36)|Unknown(2)|Substitution - Missense(1)|Deletion - Frameshift(1)	pancreas(27)|large_intestine(4)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18											41.0	42.0	41.0					18																	48603020		2203	4300	6503	46857018	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"""SMADs"""	6770	protein-coding gene	gene with protein product		600993	"""MAD, mothers against decapentaplegic homolog 4 (Drosophila)"", ""SMAD, mothers against DPP homolog 4 (Drosophila)"""	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1321C>T	18.37:g.48603020C>T	ENSP00000341551:p.Arg441Cys		46857018	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.247024	0.80024	.	.	ENSG00000141646	ENST00000342988;ENST00000398417	D;D	0.97430	-4.38;-4.38	6.03	6.03	0.97812	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.98544	0.9514	M	0.87180	2.865	0.80722	D	1	D	0.76494	0.999	D	0.64237	0.923	D	0.99143	1.0856	10	0.87932	D	0	.	19.3283	0.94273	0.0:1.0:0.0:0.0	.	441	Q13485	SMAD4_HUMAN	C	441	ENSP00000341551:R441C;ENSP00000381452:R441C	ENSP00000341551:R441C	R	+	1	0	SMAD4	46857018	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	4.556000	0.60775	2.861000	0.98227	0.655000	0.94253	CGT		0.448	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359	
SERPINB8	5271	hgsc.bcm.edu	37	18	61645698	61645698	+	Silent	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr18:61645698C>T	ENST00000397985.2	+	2	412	c.156C>T	c.(154-156)gcC>gcT	p.A52A	SERPINB8_ENST00000397988.3_Silent_p.A52A|SERPINB8_ENST00000542677.1_Intron|HMSD_ENST00000481726.1_3'UTR|SERPINB8_ENST00000353706.2_Silent_p.A52A	NM_001276490.1	NP_001263419.1	P50452	SPB8_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 8	52					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	17		Esophageal squamous(42;0.129)				GCACTGCAGCCCAGATGTCCC	0.507																																																	0			18											92.0	82.0	85.0					18																	61645698		2203	4300	6503	59796678	SO:0001819	synonymous_variant	5271			L40377	CCDS11991.1, CCDS42442.1, CCDS62460.1	18q22.1	2014-02-18	2005-08-18		ENSG00000166401	ENSG00000166401		"""Serine (or cysteine) peptidase inhibitors"""	8952	protein-coding gene	gene with protein product	"""cytoplasmic antiproteinase 2"""	601697	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 8"""	PI8		8530382, 9268635, 24172014	Standard	NM_198833		Approved	CAP2	uc002lju.3	P50452	OTTHUMG00000060596	ENST00000397985.2:c.156C>T	18.37:g.61645698C>T			59796678	B4DTW2|Q7Z2V6|Q8N178	Silent	SNP	ENST00000397985.2	37	CCDS11991.1																																																																																				0.507	SERPINB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134014.1	NM_001031848	
VHL	7428	hgsc.bcm.edu	37	3	10191600	10191600	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:10191600T>C	ENST00000256474.2	+	3	1433	c.593T>C	c.(592-594)cTg>cCg	p.L198P	VHL_ENST00000345392.2_Missense_Mutation_p.L157P|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	198			L -> Q (in pheochromocytoma). {ECO:0000269|PubMed:12000816}.|L -> R (in ECY2 and VHLD; type II).		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.L198fs*11(1)|p.L198P(1)|p.P192fs*3(1)|p.K196fs*4(1)|p.K196fs*17(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CAGAAAGACCTGGAGCGGCTG	0.488		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	5	Deletion - Frameshift(4)|Substitution - Missense(1)	kidney(4)|adrenal_gland(1)	3	GRCh37	CM020982|CM941392	VHL	M							71.0	63.0	66.0					3																	10191600		2203	4300	6503	10166600	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.593T>C	3.37:g.10191600T>C	ENSP00000256474:p.Leu198Pro		10166600	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.164919	0.78339	.	.	ENSG00000134086	ENST00000256474;ENST00000345392;ENST00000450183	D;D	0.99816	-6.91;-6.91	4.97	4.97	0.65823	von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);von Hippel-Lindau disease tumor suppressor, alpha domain (1);	0.082264	0.51477	D	0.000097	D	0.99667	0.9876	L	0.57536	1.79	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.80764	0.958;0.994	D	0.97146	0.9828	10	0.87932	D	0	-3.5946	12.9354	0.58311	0.0:0.0:0.0:1.0	.	157;198	P40337-2;P40337	.;VHL_HUMAN	P	198;157;116	ENSP00000256474:L198P;ENSP00000344757:L157P	ENSP00000256474:L198P	L	+	2	0	VHL	10166600	1.000000	0.71417	0.942000	0.38095	0.928000	0.56348	5.558000	0.67319	2.209000	0.71365	0.533000	0.62120	CTG		0.488	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551	
RFTN1	23180	hgsc.bcm.edu	37	3	16358606	16358606	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:16358606C>T	ENST00000334133.4	-	10	1738	c.1466G>A	c.(1465-1467)gGa>gAa	p.G489E	RP11-415F23.2_ENST00000607464.1_RNA|RFTN1_ENST00000483671.1_5'UTR|RFTN1_ENST00000432519.1_Missense_Mutation_p.G453E|OXNAD1_ENST00000605932.1_Intron|OXNAD1_ENST00000606098.1_Intron|OXNAD1_ENST00000544043.1_Intron|OXNAD1_ENST00000435829.2_Intron	NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	489					B cell receptor signaling pathway (GO:0050853)|dsRNA transport (GO:0033227)|growth (GO:0040007)|interleukin-17 production (GO:0032620)|membrane raft assembly (GO:0001765)|protein localization to membrane raft (GO:1903044)|protein transport into membrane raft (GO:0032596)|response to exogenous dsRNA (GO:0043330)|T cell antigen processing and presentation (GO:0002457)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 3 signaling pathway (GO:0034138)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	double-stranded RNA binding (GO:0003725)	p.G489V(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	38						TCCCATGTCTCCAGCTTTGGA	0.493																																																	1	Substitution - Missense(1)	ovary(1)	3											134.0	125.0	128.0					3																	16358606		2203	4300	6503	16333610	SO:0001583	missense	23180			D42043	CCDS33712.1	3p24.3	2010-04-09			ENSG00000131378	ENSG00000131378			30278	protein-coding gene	gene with protein product	"""raft-linking protein"""					7788527, 12805216	Standard	NM_015150		Approved	MIG2, KIAA0084, FLJ23866, Raftlin	uc003cay.3	Q14699	OTTHUMG00000156973	ENST00000334133.4:c.1466G>A	3.37:g.16358606C>T	ENSP00000334153:p.Gly489Glu		16333610	Q0D2G0|Q496Y2|Q4QQI7|Q5JB48|Q7Z7P2	Missense_Mutation	SNP	ENST00000334133.4	37	CCDS33712.1	.	.	.	.	.	.	.	.	.	.	C	12.01	1.808249	0.31961	.	.	ENSG00000131378	ENST00000432519;ENST00000334133	T;T	0.42513	0.97;1.06	5.43	1.49	0.22878	.	1.797300	0.02497	N	0.090031	T	0.49047	0.1534	L	0.57536	1.79	0.29821	N	0.83087	P;P	0.52842	0.775;0.956	B;P	0.51016	0.436;0.656	T	0.23726	-1.0180	10	0.72032	D	0.01	-8.4003	3.0083	0.06035	0.1457:0.5567:0.1409:0.1567	.	453;489	G3XAJ6;Q14699	.;RFTN1_HUMAN	E	453;489	ENSP00000403926:G453E;ENSP00000334153:G489E	ENSP00000334153:G489E	G	-	2	0	RFTN1	16333610	0.003000	0.15002	0.001000	0.08648	0.019000	0.09904	0.103000	0.15292	0.054000	0.16065	0.563000	0.77884	GGA		0.493	RFTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346908.1	NM_015150	
ZNF385D	79750	hgsc.bcm.edu	37	3	21462734	21462734	+	Missense_Mutation	SNP	T	T	C	rs113211928		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:21462734T>C	ENST00000281523.2	-	8	1678	c.1160A>G	c.(1159-1161)cAc>cGc	p.H387R		NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	387			H -> Q (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						CACAGGAGTGTGGGCGGTCCG	0.468																																																	0			3											41.0	39.0	40.0					3																	21462734		2203	4300	6503	21437738	SO:0001583	missense	79750			BC007212	CCDS2636.1	3p24.3	2012-10-05	2007-12-06	2007-12-06	ENSG00000151789	ENSG00000151789			26191	protein-coding gene	gene with protein product			"""zinc finger protein 659"""	ZNF659		12477932	Standard	NM_024697		Approved	FLJ22419	uc003cce.3	Q9H6B1	OTTHUMG00000130484	ENST00000281523.2:c.1160A>G	3.37:g.21462734T>C	ENSP00000281523:p.His387Arg		21437738		Missense_Mutation	SNP	ENST00000281523.2	37	CCDS2636.1	.	.	.	.	.	.	.	.	.	.	T	13.27	2.187296	0.38609	.	.	ENSG00000151789	ENST00000281523	T	0.34072	1.38	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.45034	0.1322	L	0.46157	1.445	0.50313	D	0.999865	D	0.59357	0.985	P	0.51974	0.686	T	0.30851	-0.9964	10	0.44086	T	0.13	-35.4295	16.1268	0.81402	0.0:0.0:0.0:1.0	.	387	Q9H6B1	Z385D_HUMAN	R	387	ENSP00000281523:H387R	ENSP00000281523:H387R	H	-	2	0	ZNF385D	21437738	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.158000	0.71851	2.213000	0.71641	0.455000	0.32223	CAC		0.468	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697	
MLH1	4292	hgsc.bcm.edu	37	3	37092043	37092043	+	Silent	SNP	T	T	C	rs63749875		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:37092043T>C	ENST00000231790.2	+	19	2386	c.2170T>C	c.(2170-2172)Ttg>Ctg	p.L724L	MLH1_ENST00000536378.1_Intron|MLH1_ENST00000435176.1_Silent_p.L626L|MLH1_ENST00000458205.2_Silent_p.L483L|MLH1_ENST00000455445.2_Silent_p.L483L|MLH1_ENST00000539477.1_Silent_p.L483L	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	724			L -> M (in HNPCC2). {ECO:0000269|PubMed:15365995}.		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						CTATAAAGCCTTGCGCTCACA	0.448		1	"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian, CNS"""	"""colorectal, endometrial, ovarian, CNS"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																														yes	Rec	yes	"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	3	3p21.3	4292	E.coli MutL homolog gene		"""E, O"""	1	Whole gene deletion(1)	ovary(1)	3	GRCh37	CM042744	MLH1	M	rs63749875						122.0	112.0	115.0					3																	37092043		2203	4300	6503	37067047	SO:0001819	synonymous_variant	4292	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"""mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)"", ""mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"""	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.2170T>C	3.37:g.37092043T>C			37067047	B4DI13|B4DQ11|E9PCU2	Silent	SNP	ENST00000231790.2	37	CCDS2663.1																																																																																				0.448	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249	
DLEC1	9940	hgsc.bcm.edu	37	3	38101313	38101313	+	Missense_Mutation	SNP	G	G	A	rs149190717	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:38101313G>A	ENST00000308059.6	+	3	664	c.643G>A	c.(643-645)Gat>Aat	p.D215N	DLEC1_ENST00000346219.3_Missense_Mutation_p.D215N|DLEC1_ENST00000452631.2_Missense_Mutation_p.D215N					deleted in lung and esophageal cancer 1									p.D215N(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		TTACTACACCGATACAGTGCC	0.493													G|||	20	0.00399361	0.0129	0.0043	5008	,	,		20302	0.0		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	skin(1)	3						G	ASN/ASP,ASN/ASP	30,3834		0,30,1902	190.0	185.0	186.0		643,643	2.0	0.0	3	dbSNP_134	186	4,8292		0,4,4144	yes	missense,missense	DLEC1	NM_007335.2,NM_007337.2	23,23	0,34,6046	AA,AG,GG		0.0482,0.7764,0.2796	probably-damaging,probably-damaging	215/1756,215/1779	38101313	34,12126	1932	4148	6080	38076317	SO:0001583	missense	9940			AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.643G>A	3.37:g.38101313G>A	ENSP00000308597:p.Asp215Asn		38076317		Missense_Mutation	SNP	ENST00000308059.6	37	CCDS2672.2	8	0.003663003663003663	5	0.01016260162601626	3	0.008287292817679558	0	0.0	0	0.0	G	9.656	1.142794	0.21205	0.007764	4.82E-4	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.05319	3.47;3.46;3.7	4.99	2.01	0.26516	.	0.782790	0.12264	N	0.484423	T	0.04907	0.0132	M	0.72894	2.215	0.09310	N	1	P;B;P	0.34546	0.456;0.171;0.456	B;B;B	0.24701	0.055;0.023;0.055	T	0.30736	-0.9968	10	0.26408	T	0.33	-5.4822	7.9747	0.30149	0.0:0.3352:0.4919:0.1729	.	215;215;215	F8W6T4;Q9Y238-3;Q9Y238	.;.;DLEC1_HUMAN	N	215	ENSP00000308597:D215N;ENSP00000315914:D215N;ENSP00000410427:D215N	ENSP00000308597:D215N	D	+	1	0	DLEC1	38076317	0.348000	0.24861	0.002000	0.10522	0.430000	0.31655	1.177000	0.31969	0.207000	0.20607	0.655000	0.94253	GAT		0.493	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
CTNNB1	1499	hgsc.bcm.edu	37	3	41266161	41266161	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:41266161A>G	ENST00000349496.5	+	3	438	c.158A>G	c.(157-159)gAg>gGg	p.E53G	CTNNB1_ENST00000396183.3_Missense_Mutation_p.E53G|CTNNB1_ENST00000396185.3_Missense_Mutation_p.E53G|CTNNB1_ENST00000405570.1_Missense_Mutation_p.E53G|CTNNB1_ENST00000453024.1_Missense_Mutation_p.E46G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	53					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.Q28_Q61del(1)|p.M1_A87del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.A5_E54del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGCAATCCTGAGGAAGAGGAT	0.478		15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)			Dom	yes		3	3p22-p21.3	1499	"""catenin (cadherin-associated protein), beta 1"""		"""E, M, O"""	111	Deletion - In frame(88)|Complex - deletion inframe(16)|Unknown(7)	liver(82)|large_intestine(16)|stomach(7)|small_intestine(2)|skin(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)	3											73.0	67.0	69.0					3																	41266161		2203	4300	6503	41241165	SO:0001583	missense	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"""Armadillo repeat containing"""	2514	protein-coding gene	gene with protein product		116806	"""catenin (cadherin-associated protein), beta 1 (88kD)"""	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.158A>G	3.37:g.41266161A>G	ENSP00000344456:p.Glu53Gly		41241165	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	17.10	3.303529	0.60195	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83	5.91	5.91	0.95273	.	0.092424	0.64402	D	0.000001	T	0.42944	0.1225	L	0.39245	1.2	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23547	-1.0185	10	0.54805	T	0.06	-0.5071	16.3453	0.83126	1.0:0.0:0.0:0.0	.	53	P35222	CTNB1_HUMAN	G	46;53;53;53;53;46;53;53;53	ENSP00000400508:E46G;ENSP00000385604:E53G;ENSP00000412219:E53G;ENSP00000379486:E53G;ENSP00000344456:E53G;ENSP00000411226:E46G;ENSP00000379488:E53G;ENSP00000409302:E53G;ENSP00000401599:E53G	ENSP00000344456:E53G	E	+	2	0	CTNNB1	41241165	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	9.339000	0.96797	2.261000	0.74972	0.533000	0.62120	GAG		0.478	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210	
SETD2	29072	hgsc.bcm.edu	37	3	47161980	47161980	+	Silent	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:47161980A>G	ENST00000409792.3	-	3	4188	c.4146T>C	c.(4144-4146)gcT>gcC	p.A1382A		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1382					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.A879A(2)|p.A1382A(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TTTCATTCACAGCTAAAGTGT	0.363			"""N, F, S, Mis"""		clear cell renal carcinoma																																			Rec	yes		3	3p21.31	29072	SET domain containing 2		E	3	Substitution - coding silent(3)	kidney(3)	3											64.0	65.0	65.0					3																	47161980		2203	4300	6503	47136984	SO:0001819	synonymous_variant	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4146T>C	3.37:g.47161980A>G			47136984	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Silent	SNP	ENST00000409792.3	37	CCDS2749.2																																																																																				0.363	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
GRM2	2912	hgsc.bcm.edu	37	3	51749544	51749544	+	Silent	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:51749544G>A	ENST00000395052.3	+	4	1989	c.1755G>A	c.(1753-1755)gtG>gtA	p.V585V	GRM2_ENST00000442933.2_Intron|GRM2_ENST00000475478.1_3'UTR	NM_000839.3	NP_000830.2	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2	585					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|glutamate secretion (GO:0014047)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CCCTCTTTGTGCTGGGTGTCT	0.627																																																	0			3											79.0	76.0	77.0					3																	51749544		2203	4300	6503	51724584	SO:0001819	synonymous_variant	2912			L35318	CCDS2834.1	3p21.2	2013-09-20			ENSG00000164082	ENSG00000164082		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4594	protein-coding gene	gene with protein product		604099				7620613	Standard	NM_000839		Approved	GPRC1B, mGlu2, MGLUR2	uc010hlv.3	Q14416	OTTHUMG00000156902	ENST00000395052.3:c.1755G>A	3.37:g.51749544G>A			51724584	B0M0K7|Q14CU5|Q52MC6|Q9H3N6	Silent	SNP	ENST00000395052.3	37	CCDS2834.1																																																																																				0.627	GRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346542.1		
DUSP7	1849	hgsc.bcm.edu	37	3	52084905	52084905	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:52084905A>G	ENST00000495880.1	-	3	1369	c.1186T>C	c.(1186-1188)Tcg>Ccg	p.S396P	DUSP7_ENST00000296483.6_Missense_Mutation_p.S345P			Q16829	DUS7_HUMAN	dual specificity phosphatase 7	396					inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of MAP kinase activity (GO:0043407)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	17				BRCA - Breast invasive adenocarcinoma(193;5.14e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		TGCTCACTCGACGCGTGGTTG	0.597																																																	0			3											167.0	130.0	142.0					3																	52084905		2203	4300	6503	52059945	SO:0001583	missense	1849			X93921	CCDS33766.1, CCDS33766.2	3p21	2011-06-09			ENSG00000164086	ENSG00000164086		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3073	protein-coding gene	gene with protein product		602749				8626780, 9205128	Standard	NM_001947		Approved	MKP-X, PYST2	uc003dct.3	Q16829	OTTHUMG00000157819	ENST00000495880.1:c.1186T>C	3.37:g.52084905A>G	ENSP00000417183:p.Ser396Pro		52059945	Q2M3J7|Q8NFJ0	Missense_Mutation	SNP	ENST00000495880.1	37	CCDS33766.2	.	.	.	.	.	.	.	.	.	.	a	1.283	-0.609654	0.03690	.	.	ENSG00000164086	ENST00000495880;ENST00000296483	T;T	0.02421	4.3;4.3	5.75	4.89	0.63831	.	0.165531	0.53938	N	0.000043	T	0.01387	0.0045	N	0.02247	-0.625	0.23661	N	0.997172	B	0.02656	0.0	B	0.06405	0.002	T	0.45338	-0.9268	10	0.02654	T	1	.	14.5032	0.67737	0.0713:0.0:0.9287:0.0	.	396	Q16829	DUS7_HUMAN	P	396;345	ENSP00000417183:S396P;ENSP00000296483:S345P	ENSP00000296483:S345P	S	-	1	0	DUSP7	52059945	1.000000	0.71417	0.883000	0.34634	0.481000	0.33189	5.699000	0.68310	1.452000	0.47756	-0.138000	0.14375	TCG		0.597	DUSP7-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349697.1	NM_001947	
PTPRG	5793	hgsc.bcm.edu	37	3	62189578	62189578	+	Silent	SNP	C	C	T	rs371158794		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:62189578C>T	ENST00000474889.1	+	12	2486	c.2109C>T	c.(2107-2109)cgC>cgT	p.R703R	PTPRG_ENST00000295874.10_Silent_p.R703R	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	703					brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R703R(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		CTATGTCCCGCGGGGACCGAT	0.542																																																	1	Substitution - coding silent(1)	ovary(1)	3																																								62164618	SO:0001819	synonymous_variant	5793			L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.2109C>T	3.37:g.62189578C>T			62164618	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Silent	SNP	ENST00000474889.1	37	CCDS2895.1																																																																																				0.542	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841	
ATP6V1A	523	hgsc.bcm.edu	37	3	113517280	113517280	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:113517280A>G	ENST00000273398.3	+	12	1589	c.1481A>G	c.(1480-1482)cAg>cGg	p.Q494R	ATP6V1A_ENST00000538620.1_Missense_Mutation_p.Q461R	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	494					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	ATP binding (GO:0005524)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Alendronate(DB00630)|Etidronic acid(DB01077)|Tiludronate(DB01133)	GAAATTGTACAGCTTGTGGGA	0.423																																																	0			3											76.0	78.0	77.0					3																	113517280		2203	4300	6503	114999970	SO:0001583	missense	523			L09235	CCDS2976.1	3q13.31	2010-04-21	2002-08-29	2003-04-25	ENSG00000114573	ENSG00000114573	3.6.3.14	"""ATPases / V-type"""	851	protein-coding gene	gene with protein product		607027	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha polypeptide, 70kD, isoform 1"""	VPP2, ATP6A1, ATP6V1A1		8463241	Standard	NM_001690		Approved	Vma1, VA68	uc003eao.3	P38606	OTTHUMG00000159295	ENST00000273398.3:c.1481A>G	3.37:g.113517280A>G	ENSP00000273398:p.Gln494Arg		114999970	B2RBR8|B7Z1R5|D3DN75|Q53YD9|Q96DY6|Q9UHY3	Missense_Mutation	SNP	ENST00000273398.3	37	CCDS2976.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.018282	0.75275	.	.	ENSG00000114573	ENST00000545842;ENST00000273398;ENST00000538620	D;D	0.81739	-1.53;-1.53	4.93	4.93	0.64822	ATPase, F1/V1/A1 complex, alpha/beta subunit, C-terminal (2);ATPase, F1 complex beta subunit/V1 complex, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.88310	0.6402	M	0.74258	2.255	0.80722	D	1	D	0.67145	0.996	D	0.72075	0.976	D	0.87567	0.2475	10	0.34782	T	0.22	-9.3633	14.8767	0.70498	1.0:0.0:0.0:0.0	.	494	P38606	VATA_HUMAN	R	211;494;461	ENSP00000273398:Q494R;ENSP00000439874:Q461R	ENSP00000273398:Q494R	Q	+	2	0	ATP6V1A	114999970	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.886000	0.92447	1.983000	0.57843	0.459000	0.35465	CAG		0.423	ATP6V1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354457.1	NM_001690	
GAP43	2596	hgsc.bcm.edu	37	3	115439655	115439655	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:115439655A>G	ENST00000305124.6	+	3	1009	c.643A>G	c.(643-645)Acc>Gcc	p.T215A	GAP43_ENST00000393780.3_Missense_Mutation_p.T251A	NM_002045.3	NP_002036.1	P17677	NEUM_HUMAN	growth associated protein 43	215					axon choice point recognition (GO:0016198)|cell fate commitment (GO:0045165)|glial cell differentiation (GO:0010001)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of filopodium assembly (GO:0051489)|regulation of growth (GO:0040008)|response to wounding (GO:0009611)|tissue regeneration (GO:0042246)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	32				GBM - Glioblastoma multiforme(114;0.164)		TGTAGATGAAACCAAACCTAA	0.438																																																	0			3											197.0	207.0	204.0					3																	115439655		2203	4300	6503	116922345	SO:0001583	missense	2596				CCDS33830.1, CCDS46890.1	3q13.31	2013-09-19			ENSG00000172020	ENSG00000172020			4140	protein-coding gene	gene with protein product	"""neuron growth-associated protein 43"", ""neuromodulin"", ""nerve growth-related peptide GAP43"", ""axonal membrane protein GAP-43"", ""protein F1"", ""calmodulin-binding protein P-57"", ""neural phosphoprotein B-50"""	162060				3272162, 8231732	Standard	NM_002045		Approved	B-50, PP46	uc003ebr.2	P17677	OTTHUMG00000133758	ENST00000305124.6:c.643A>G	3.37:g.115439655A>G	ENSP00000305010:p.Thr215Ala		116922345	A8K0Y4	Missense_Mutation	SNP	ENST00000305124.6	37	CCDS33830.1	.	.	.	.	.	.	.	.	.	.	A	12.92	2.082186	0.36758	.	.	ENSG00000172020	ENST00000305124;ENST00000393780	T;T	0.58506	0.33;0.33	5.7	4.55	0.56014	Neuromodulin (GAP-43), C-terminal (1);	0.226724	0.36444	N	0.002599	T	0.47210	0.1433	L	0.33485	1.01	0.41085	D	0.985558	B;B	0.25048	0.117;0.117	B;B	0.29524	0.103;0.044	T	0.41734	-0.9492	10	0.46703	T	0.11	-3.9186	10.8563	0.46800	0.9254:0.0:0.0746:0.0	.	251;215	A8K0Y4;P17677	.;NEUM_HUMAN	A	215;251	ENSP00000305010:T215A;ENSP00000377372:T251A	ENSP00000305010:T215A	T	+	1	0	GAP43	116922345	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.868000	0.56055	1.002000	0.39104	0.482000	0.46254	ACC		0.438	GAP43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258216.2	NM_002045	
CD80	941	hgsc.bcm.edu	37	3	119256010	119256010	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:119256010A>G	ENST00000264246.3	-	4	1036	c.674T>C	c.(673-675)gTg>gCg	p.V225A	CD80_ENST00000383669.3_Missense_Mutation_p.V225A|CD80_ENST00000478182.1_Missense_Mutation_p.V225A|CD80_ENST00000383668.3_Intron	NM_005191.3	NP_005182.1	P33681	CD80_HUMAN	CD80 molecule	225	Ig-like C2-type.				cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of signal transduction (GO:0009967)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|viral process (GO:0016032)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)	p.V225E(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	12					Abatacept(DB01281)|Belatacept(DB06681)	GGTCTGATTCACTCTTAAATG	0.373																																					Melanoma(132;135 1764 1806 5833 14593)												1	Substitution - Missense(1)	ovary(1)	3											203.0	192.0	196.0					3																	119256010		2203	4300	6503	120738700	SO:0001583	missense	941				CCDS2989.1	3q13.3-q21	2013-01-11	2006-03-31		ENSG00000121594	ENSG00000121594		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	1700	protein-coding gene	gene with protein product	"""B-lymphocyte activation antigen B7"""	112203	"""CD80 antigen (CD28 antigen ligand 1, B7-1 antigen)"", ""CD80 molecule """	CD28LG, CD28LG1		1370389	Standard	NM_005191		Approved	B7.1, B7-1	uc003ecq.3	P33681	OTTHUMG00000159419	ENST00000264246.3:c.674T>C	3.37:g.119256010A>G	ENSP00000264246:p.Val225Ala		120738700	Q5DTA9|Q5DTB0	Missense_Mutation	SNP	ENST00000264246.3	37	CCDS2989.1	.	.	.	.	.	.	.	.	.	.	A	18.32	3.598053	0.66332	.	.	ENSG00000121594	ENST00000264246;ENST00000478182;ENST00000383669	T;T;T	0.75367	-0.93;-0.93;-0.93	5.19	5.19	0.71726	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.46442	D	0.000295	D	0.84611	0.5510	M	0.80982	2.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.994;0.995	D	0.83873	0.0275	10	0.33141	T	0.24	-18.903	11.3641	0.49662	1.0:0.0:0.0:0.0	.	225;225	Q5DTB0;P33681	.;CD80_HUMAN	A	225	ENSP00000264246:V225A;ENSP00000418364:V225A;ENSP00000373165:V225A	ENSP00000264246:V225A	V	-	2	0	CD80	120738700	0.888000	0.30383	0.788000	0.31933	0.047000	0.14425	3.987000	0.56944	2.175000	0.68902	0.528000	0.53228	GTG		0.373	CD80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355196.1	NM_005191	
FBXO40	51725	hgsc.bcm.edu	37	3	121345659	121345659	+	Missense_Mutation	SNP	C	C	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:121345659C>A	ENST00000338040.4	+	4	2446	c.2032C>A	c.(2032-2034)Ccg>Acg	p.P678T		NM_016298.3	NP_057382.2	Q9UH90	FBX40_HUMAN	F-box protein 40	678					muscle cell differentiation (GO:0042692)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P678T(1)		NS(1)|breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(11)|lung(19)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	46				GBM - Glioblastoma multiforme(114;0.189)		CAAAACTGACCCGATTCTTTT	0.478																																																	1	Substitution - Missense(1)	ovary(1)	3											115.0	111.0	113.0					3																	121345659		2203	4300	6503	122828349	SO:0001583	missense	51725			AF204674	CCDS33835.1	3q21.1	2004-08-24			ENSG00000163833	ENSG00000163833		"""F-boxes /  ""other"""""	29816	protein-coding gene	gene with protein product		609107				10574462	Standard	NM_016298		Approved	KIAA1195, Fbx40	uc003eeg.2	Q9UH90	OTTHUMG00000159410	ENST00000338040.4:c.2032C>A	3.37:g.121345659C>A	ENSP00000337510:p.Pro678Thr		122828349	B2RAX7|Q32M70|Q9ULM5	Missense_Mutation	SNP	ENST00000338040.4	37	CCDS33835.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.035186	0.93575	.	.	ENSG00000163833	ENST00000338040	T	0.35973	1.28	6.17	6.17	0.99709	.	0.050909	0.85682	D	0.000000	T	0.61085	0.2319	M	0.68593	2.085	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.59225	-0.7494	10	0.66056	D	0.02	-15.0266	18.3732	0.90420	0.0:1.0:0.0:0.0	.	678	Q9UH90	FBX40_HUMAN	T	678	ENSP00000337510:P678T	ENSP00000337510:P678T	P	+	1	0	FBXO40	122828349	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	3.973000	0.56845	2.941000	0.99782	0.655000	0.94253	CCG		0.478	FBXO40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355158.1	NM_016298	
UROC1	131669	hgsc.bcm.edu	37	3	126228489	126228489	+	Missense_Mutation	SNP	G	G	A	rs556450823	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:126228489G>A	ENST00000290868.2	-	3	343	c.290C>T	c.(289-291)aCg>aTg	p.T97M	UROC1_ENST00000383579.3_Missense_Mutation_p.T97M	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN	urocanate hydratase 1	97					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	urocanate hydratase activity (GO:0016153)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(1)|skin(1)	39				GBM - Glioblastoma multiforme(114;0.17)		AGCCACTTTCGTCTGGCAGGG	0.612													G|||	2	0.000399361	0.0	0.0	5008	,	,		16032	0.0		0.0	False		,,,				2504	0.002																0			3											42.0	30.0	34.0					3																	126228489		2128	4118	6246	127711179	SO:0001583	missense	131669			AK055862	CCDS3038.1, CCDS54636.1	3q21.2	2012-08-21	2012-08-21		ENSG00000159650	ENSG00000159650	4.2.1.49		26444	protein-coding gene	gene with protein product	"""urocanase 1"""	613012	"""urocanase domain containing 1"""			19304569	Standard	NM_144639		Approved	FLJ31300, HMFN0320	uc010hsi.2	Q96N76	OTTHUMG00000162753	ENST00000290868.2:c.290C>T	3.37:g.126228489G>A	ENSP00000290868:p.Thr97Met		127711179	E9PE13|Q14C64|Q68CJ7	Missense_Mutation	SNP	ENST00000290868.2	37	CCDS3038.1	.	.	.	.	.	.	.	.	.	.	G	12.77	2.037377	0.35989	.	.	ENSG00000159650	ENST00000290868;ENST00000383579	T;T	0.44482	0.92;0.92	5.13	2.36	0.29203	Urocanase domain (2);	0.216752	0.47093	N	0.000253	T	0.62962	0.2471	M	0.85299	2.745	0.48395	D	0.999646	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.954	T	0.63646	-0.6590	10	0.87932	D	0	-1.7954	7.8133	0.29243	0.2743:0.0:0.7257:0.0	.	97;97	E9PE13;Q96N76	.;HUTU_HUMAN	M	97	ENSP00000290868:T97M;ENSP00000373073:T97M	ENSP00000290868:T97M	T	-	2	0	UROC1	127711179	1.000000	0.71417	0.497000	0.27552	0.013000	0.08279	3.002000	0.49496	0.562000	0.29204	-0.339000	0.08088	ACG		0.612	UROC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370325.2	NM_144639	
TRPC1	7220	hgsc.bcm.edu	37	3	142455330	142455330	+	Silent	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:142455330C>T	ENST00000476941.1	+	2	768	c.282C>T	c.(280-282)aaC>aaT	p.N94N	TRPC1_ENST00000273482.6_Silent_p.N94N	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	94					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						CTATTGAAAACGAAAACTTGG	0.363																																																	0			3											174.0	175.0	174.0					3																	142455330		2203	4300	6503	143938020	SO:0001819	synonymous_variant	7220			X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.282C>T	3.37:g.142455330C>T			143938020	Q14CE4	Silent	SNP	ENST00000476941.1	37	CCDS58856.1																																																																																				0.363	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304	
SKIL	6498	hgsc.bcm.edu	37	3	170110052	170110052	+	Silent	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:170110052A>G	ENST00000458537.3	+	6	2611	c.1902A>G	c.(1900-1902)gcA>gcG	p.A634A	SKIL_ENST00000413427.2_Silent_p.A588A|SKIL_ENST00000259119.4_Silent_p.A634A|SKIL_ENST00000426052.2_Silent_p.A614A	NM_001145097.2|NM_001248008.1|NM_005414.4	NP_001138569.1|NP_001234937.1|NP_005405.2	P12757	SKIL_HUMAN	SKI-like proto-oncogene	634					blastocyst formation (GO:0001825)|cell cycle arrest (GO:0007050)|gene expression (GO:0010467)|lens fiber cell differentiation (GO:0070306)|lymphocyte homeostasis (GO:0002260)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of axonogenesis (GO:0050772)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|protein heterotrimerization (GO:0070208)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|response to antibiotic (GO:0046677)|response to cytokine (GO:0034097)|response to growth factor (GO:0070848)|skeletal muscle tissue development (GO:0007519)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	25	all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			CATAGTTGGCAGAACTGAGGC	0.363																																																	0			3											86.0	90.0	89.0					3																	170110052		2203	4300	6503	171592746	SO:0001819	synonymous_variant	6498			X15217	CCDS33890.1, CCDS46953.1, CCDS46954.1	3q26	2014-06-25	2014-06-25		ENSG00000136603	ENSG00000136603		"""SKI transcriptional corepressors"""	10897	protein-coding gene	gene with protein product		165340	"""SKI-like oncogene"""			2762147	Standard	NM_005414		Approved	SNO, SnoN, SnoA	uc003fgw.3	P12757	OTTHUMG00000158831	ENST00000458537.3:c.1902A>G	3.37:g.170110052A>G			171592746	A6NGT1|B4DT50|O00464|P12756|Q07501	Silent	SNP	ENST00000458537.3	37	CCDS33890.1																																																																																				0.363	SKIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352351.4	NM_005414	
FNDC3B	64778	hgsc.bcm.edu	37	3	172065127	172065127	+	Silent	SNP	T	T	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:172065127T>A	ENST00000336824.4	+	21	2589	c.2490T>A	c.(2488-2490)gcT>gcA	p.A830A	FNDC3B_ENST00000416957.1_Silent_p.A830A|FNDC3B_ENST00000415807.2_Silent_p.A830A	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	830	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		TGTTGCCTGCTGCACAGTATT	0.443																																																	0			3											97.0	91.0	93.0					3																	172065127		2203	4300	6503	173547821	SO:0001819	synonymous_variant	64778			AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"""Fibronectin type III domain containing"""	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.2490T>A	3.37:g.172065127T>A			173547821	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Silent	SNP	ENST00000336824.4	37	CCDS3217.1																																																																																				0.443	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763	
PIK3CA	5290	hgsc.bcm.edu	37	3	178952076	178952076	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:178952076A>G	ENST00000263967.3	+	21	3288	c.3131A>G	c.(3130-3132)aAt>aGt	p.N1044S	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1044	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.N1044S(2)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AAACAAATGAATGATGCACAT	0.373		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)			Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	2	Substitution - Missense(2)	ovary(1)|central_nervous_system(1)	3											99.0	89.0	92.0					3																	178952076		1910	4124	6034	180434770	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3131A>G	3.37:g.178952076A>G	ENSP00000263967:p.Asn1044Ser		180434770	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.813104	0.50527	.	.	ENSG00000121879	ENST00000263967	T	0.81078	-1.45	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.73466	0.3590	L	0.39566	1.225	0.80722	D	1	P	0.45078	0.85	B	0.39339	0.297	T	0.71708	-0.4511	10	0.19590	T	0.45	-24.648	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1044	P42336	PK3CA_HUMAN	S	1044	ENSP00000263967:N1044S	ENSP00000263967:N1044S	N	+	2	0	PIK3CA	180434770	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	AAT		0.373	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
EHHADH	1962	hgsc.bcm.edu	37	3	184910747	184910747	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:184910747A>G	ENST00000231887.3	-	7	1514	c.1439T>C	c.(1438-1440)gTg>gCg	p.V480A	EHHADH_ENST00000456310.1_Missense_Mutation_p.V384A|EHHADH-AS1_ENST00000417720.1_RNA	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	480	3-hydroxyacyl-CoA dehydrogenase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			TCGATTCCCCACAAATCCAAA	0.418																																																	0			3											108.0	109.0	108.0					3																	184910747		2203	4300	6503	186393441	SO:0001583	missense	1962			L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"""enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"""	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.1439T>C	3.37:g.184910747A>G	ENSP00000231887:p.Val480Ala		186393441	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	37	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.703750	0.68501	.	.	ENSG00000113790	ENST00000231887;ENST00000456310	D;D	0.91124	-2.79;-2.79	5.91	5.91	0.95273	3-hydroxyacyl-CoA dehydrogenase, C-terminal (1);3-hydroxyacyl-CoA dehydrogenase, conserved site (1);Dehydrogenase, multihelical (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.117554	0.56097	D	0.000023	D	0.93897	0.8047	L	0.61387	1.9	0.80722	D	1	D	0.67145	0.996	D	0.65010	0.931	D	0.93489	0.6834	10	0.44086	T	0.13	-29.7634	16.3483	0.83171	1.0:0.0:0.0:0.0	.	480	Q08426	ECHP_HUMAN	A	480;384	ENSP00000231887:V480A;ENSP00000387746:V384A	ENSP00000231887:V480A	V	-	2	0	EHHADH	186393441	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.845000	0.69437	2.254000	0.74563	0.533000	0.62120	GTG		0.418	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1		
TRA2B	6434	hgsc.bcm.edu	37	3	185643399	185643399	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:185643399T>C	ENST00000453386.2	-	3	461	c.186A>G	c.(184-186)agA>agG	p.R62R	TRA2B_ENST00000471134.1_5'Flank|TRA2B_ENST00000382191.4_5'UTR	NM_004593.2	NP_004584.1	P62995	TRA2B_HUMAN	transformer 2 beta homolog (Drosophila)	62	Arg/Ser-rich (RS1 domain).				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(3)|prostate(1)|urinary_tract(1)	18						TTCGGGAGCTTCTTCTGGATC	0.458																																																	0			3											94.0	92.0	93.0					3																	185643399		2203	4300	6503	187126093	SO:0001819	synonymous_variant	6434			AF057159	CCDS33905.1, CCDS58872.1	3q26.2-q27	2014-06-13	2009-02-27	2009-02-27	ENSG00000136527	ENSG00000136527		"""RNA binding motif (RRM) containing"""	10781	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 156"""	602719	"""splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila)"""	SFRS10		9790768	Standard	NM_004593		Approved	Htra2-beta, PPP1R156	uc003fpv.3	P62995	OTTHUMG00000156641	ENST00000453386.2:c.186A>G	3.37:g.185643399T>C			187126093	B4DVK2|D3DNU3|O15449|Q15815|Q64283	Silent	SNP	ENST00000453386.2	37	CCDS33905.1																																																																																				0.458	TRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344984.1	NM_004593	
ETV5	2119	hgsc.bcm.edu	37	3	185783741	185783741	+	Silent	SNP	C	C	T	rs370362112		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:185783741C>T	ENST00000306376.5	-	8	1017	c.771G>A	c.(769-771)ccG>ccA	p.P257P	ETV5_ENST00000480706.1_5'Flank|ETV5_ENST00000434744.1_Silent_p.P257P|ETV5_ENST00000537818.1_Silent_p.P299P	NM_004454.2	NP_004445.1	P41161	ETV5_HUMAN	ets variant 5	257					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|locomotory behavior (GO:0007626)|male germ-line stem cell asymmetric division (GO:0048133)|neuromuscular synaptic transmission (GO:0007274)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of synapse organization (GO:0050807)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	28	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			CCTGAGGGGGCGGGGGAGCTG	0.587			T	"""TMPRSS2, SCL45A3"""	Prostate																																			Dom	yes		3	3q28	2119	ets variant gene 5		E	0			3						C		0,4406		0,0,2203	55.0	63.0	60.0		771	-10.6	0.8	3		60	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ETV5	NM_004454.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		257/511	185783741	1,13005	2203	4300	6503	187266435	SO:0001819	synonymous_variant	2119			BC007333	CCDS33906.1	3q28	2008-09-12	2008-09-12		ENSG00000244405	ENSG00000244405			3494	protein-coding gene	gene with protein product	"""ets-related molecule"""	601600	"""ets variant gene 5 (ets-related molecule)"""			8152800	Standard	NM_004454		Approved	ERM	uc003fpz.3	P41161	OTTHUMG00000156639	ENST00000306376.5:c.771G>A	3.37:g.185783741C>T			187266435	A6NH46|B7Z7D7|Q6IBN5	Silent	SNP	ENST00000306376.5	37	CCDS33906.1																																																																																				0.587	ETV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344947.1	NM_004454	
TEAD4	7004	hgsc.bcm.edu	37	12	3147233	3147233	+	Nonsense_Mutation	SNP	A	A	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:3147233A>T	ENST00000397122.2	+	9	895	c.610A>T	c.(610-612)Aag>Tag	p.K204*	TEAD4_ENST00000359864.2_Nonsense_Mutation_p.K333*|TEAD4_ENST00000358409.2_Nonsense_Mutation_p.K290*	NM_201443.2	NP_958851.1	Q15561	TEAD4_HUMAN	TEA domain family member 4	333					gene expression (GO:0010467)|hippo signaling (GO:0035329)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	Ovarian(42;0.211)		OV - Ovarian serous cystadenocarcinoma(31;0.000563)|COAD - Colon adenocarcinoma(12;0.0831)			CTGCTCCACGAAGGTCTGCTC	0.587																																																	0			12											89.0	79.0	83.0					12																	3147233		2203	4300	6503	3017494	SO:0001587	stop_gained	7004			X94438	CCDS31729.1, CCDS31730.1, CCDS41737.1	12p13.3-p13.2	2008-05-14				ENSG00000197905			11717	protein-coding gene	gene with protein product		601714		TCF13L1		9889009, 8921372	Standard	NM_003213		Approved	TEF-3, TEFR-1, EFTR-2, RTEF-1	uc010sej.2	Q15561		ENST00000397122.2:c.610A>T	12.37:g.3147233A>T	ENSP00000380311:p.Lys204*		3017494	H0Y308|Q6MZR9|Q8NEV5|Q92883|Q96BK2	Nonsense_Mutation	SNP	ENST00000397122.2	37	CCDS41737.1	.	.	.	.	.	.	.	.	.	.	A	38	7.162676	0.98107	.	.	ENSG00000197905	ENST00000358409;ENST00000359864;ENST00000397122	.	.	.	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-28.6861	13.4969	0.61432	1.0:0.0:0.0:0.0	.	.	.	.	X	290;333;204	.	ENSP00000351184:K290X	K	+	1	0	TEAD4	3017494	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	9.295000	0.96095	1.773000	0.52216	0.533000	0.62120	AAG		0.587	TEAD4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398477.1	NM_003213	
CD163L1	283316	hgsc.bcm.edu	37	12	7586120	7586120	+	Missense_Mutation	SNP	G	G	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:7586120G>T	ENST00000313599.3	-	3	352	c.295C>A	c.(295-297)Cgt>Agt	p.R99S	CD163L1_ENST00000416109.2_Missense_Mutation_p.R99S|CD163L1_ENST00000396630.1_Missense_Mutation_p.R99S			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	99	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						TGTCCAAAACGAAACATGGCG	0.478																																																	0			12											123.0	97.0	106.0					12																	7586120		2203	4300	6503	7477387	SO:0001583	missense	283316			AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"""CD163 antigen-like 1"""			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.295C>A	12.37:g.7586120G>T	ENSP00000315945:p.Arg99Ser		7477387	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	SNP	ENST00000313599.3	37	CCDS8577.1	.	.	.	.	.	.	.	.	.	.	G	0.382	-0.928373	0.02359	.	.	ENSG00000177675	ENST00000313599;ENST00000416109;ENST00000396630;ENST00000543276	T;T;T;T	0.33438	1.41;1.41;1.41;3.51	1.64	0.641	0.17759	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	2.179770	0.03610	U	0.234674	T	0.13586	0.0329	N	0.03917	-0.325	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.21895	-1.0232	10	0.07813	T	0.8	.	8.1402	0.31078	0.0:0.3695:0.6304:0.0	.	99;99	E7EVK4;Q9NR16	.;C163B_HUMAN	S	99;99;99;3	ENSP00000315945:R99S;ENSP00000393474:R99S;ENSP00000379871:R99S;ENSP00000442328:R3S	ENSP00000315945:R99S	R	-	1	0	CD163L1	7477387	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.362000	0.07602	0.156000	0.19299	-0.414000	0.06135	CGT		0.478	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941	
C12orf40	283461	hgsc.bcm.edu	37	12	40114805	40114805	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:40114805T>C	ENST00000324616.5	+	13	1865	c.1711T>C	c.(1711-1713)Tgc>Cgc	p.C571R		NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	571								p.C571G(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						ACAGTTGCAGTGCAATTCAGC	0.383																																																	1	Substitution - Missense(1)	ovary(1)	12											95.0	90.0	92.0					12																	40114805		1922	4136	6058	38401072	SO:0001583	missense	283461			AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.1711T>C	12.37:g.40114805T>C	ENSP00000317671:p.Cys571Arg		38401072	B7WNU1|Q8IXY6|Q8N818|V9HW02	Missense_Mutation	SNP	ENST00000324616.5	37	CCDS41770.1	.	.	.	.	.	.	.	.	.	.	T	12.57	1.976734	0.34848	.	.	ENSG00000180116	ENST00000324616	T	0.49720	0.77	4.95	0.83	0.18854	.	0.543405	0.18058	N	0.153036	T	0.37839	0.1018	L	0.32530	0.975	0.24512	N	0.994207	P	0.43701	0.815	P	0.48921	0.595	T	0.27088	-1.0084	10	0.72032	D	0.01	.	1.465	0.02404	0.2136:0.0941:0.159:0.5333	.	571	Q86WS4	CL040_HUMAN	R	571	ENSP00000317671:C571R	ENSP00000317671:C571R	C	+	1	0	C12orf40	38401072	0.000000	0.05858	0.077000	0.20336	0.012000	0.07955	-0.490000	0.06482	0.023000	0.15187	0.477000	0.44152	TGC		0.383	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599	
PRICKLE1	144165	hgsc.bcm.edu	37	12	42858556	42858556	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:42858556A>G	ENST00000455697.1	-	7	1565	c.1280T>C	c.(1279-1281)cTc>cCc	p.L427P	PRICKLE1_ENST00000445766.2_Missense_Mutation_p.L427P|RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000548696.1_Missense_Mutation_p.L427P|PRICKLE1_ENST00000345127.3_Missense_Mutation_p.L427P|PRICKLE1_ENST00000552240.1_Missense_Mutation_p.L427P	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	427					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		TGGCTGAAAGAGGCTTTTATC	0.438																																																	0			12											70.0	73.0	72.0					12																	42858556		2203	4300	6503	41144823	SO:0001583	missense	144165			AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"""prickle-like 1 (Drosophila)"""			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.1280T>C	12.37:g.42858556A>G	ENSP00000401060:p.Leu427Pro		41144823	Q14C83|Q71QF8|Q96N00	Missense_Mutation	SNP	ENST00000455697.1	37	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	A	14.89	2.669468	0.47677	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	T;T;T;T;T	0.62232	0.04;0.04;0.04;0.04;0.04	5.76	4.62	0.57501	.	0.178326	0.52532	D	0.000078	T	0.40815	0.1132	N	0.08118	0	0.80722	D	1	B	0.12630	0.006	B	0.12156	0.007	T	0.17715	-1.0360	10	0.30078	T	0.28	-4.2574	11.811	0.52183	0.9316:0.0:0.0684:0.0	.	427	Q96MT3	PRIC1_HUMAN	P	427	ENSP00000401060:L427P;ENSP00000398947:L427P;ENSP00000448359:L427P;ENSP00000345064:L427P;ENSP00000449819:L427P	ENSP00000345064:L427P	L	-	2	0	PRICKLE1	41144823	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.910000	0.92685	1.119000	0.41883	0.528000	0.53228	CTC		0.438	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1		
MAP3K12	7786	hgsc.bcm.edu	37	12	53875791	53875791	+	Silent	SNP	T	T	C	rs552979863		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:53875791T>C	ENST00000267079.2	-	14	2640	c.2415A>G	c.(2413-2415)tcA>tcG	p.S805S	MAP3K12_ENST00000547035.1_Silent_p.S838S|MAP3K12_ENST00000547488.1_Silent_p.S838S	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12	805					histone phosphorylation (GO:0016572)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	37						GGATGACCTCTGAAGGAGGTG	0.562											OREG0021873	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0			12											101.0	94.0	96.0					12																	53875791		2203	4300	6503	52162058	SO:0001819	synonymous_variant	7786			U07358	CCDS8860.1, CCDS55831.1	12q13.13	2013-10-30			ENSG00000139625	ENSG00000139625		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6851	protein-coding gene	gene with protein product	"""dual leucine zipper kinase DLK"""	600447		ZPK		8037767	Standard	NM_006301		Approved	MUK, DLK, ZPKP1, MEKK12	uc001sdn.2	Q12852	OTTHUMG00000169854	ENST00000267079.2:c.2415A>G	12.37:g.53875791T>C		996	52162058	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Silent	SNP	ENST00000267079.2	37	CCDS8860.1																																																																																				0.562	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301	
PTPN11	5781	hgsc.bcm.edu	37	12	112888165	112888165	+	Missense_Mutation	SNP	G	G	T	rs397507508|rs397507510		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:112888165G>T	ENST00000351677.2	+	3	379	c.181G>T	c.(181-183)Gat>Tat	p.D61Y	PTPN11_ENST00000392597.1_Missense_Mutation_p.D61Y	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	61	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.		D -> G (in NS1). {ECO:0000269|PubMed:11704759, ECO:0000269|PubMed:11992261, ECO:0000269|PubMed:12161469, ECO:0000269|PubMed:12634870}.|D -> N (in NS1). {ECO:0000269|PubMed:11992261, ECO:0000269|PubMed:12634870}.|D -> V (in JMML; also in myelodysplastic syndrome). {ECO:0000269|PubMed:12717436}.|D -> Y (in JMML). {ECO:0000269|PubMed:12717436}.		abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.D61Y(29)|p.D61H(3)|p.D61N(2)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						GAACACTGGTGATTACTATGA	0.423			Mis		"""JMML, AML, MDS"""		Noonan Syndrome		Noonan syndrome																															Dom	yes		12	12q24.1	5781	"""protein tyrosine phosphatase, non-receptor type 11"""	yes	L	34	Substitution - Missense(34)	haematopoietic_and_lymphoid_tissue(34)	12	GRCh37	CD055729|CM021127	PTPN11	D|M							143.0	134.0	137.0					12																	112888165		2203	4300	6503	111372548	SO:0001583	missense	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"", ""SH2 domain containing"""	9644	protein-coding gene	gene with protein product		176876	"""Noonan syndrome 1"""	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.181G>T	12.37:g.112888165G>T	ENSP00000340944:p.Asp61Tyr		111372548	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	37	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	G	32	5.132218	0.94473	.	.	ENSG00000179295	ENST00000392597;ENST00000351677;ENST00000392596	D;D	0.96774	-4.12;-4.12	5.9	5.9	0.94986	.	0.046067	0.85682	D	0.000000	D	0.98451	0.9484	M	0.87456	2.885	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	D	0.98880	1.0769	10	0.87932	D	0	.	20.2787	0.98501	0.0:0.0:1.0:0.0	.	61;61	Q06124-2;Q06124-3	.;.	Y	61	ENSP00000376376:D61Y;ENSP00000340944:D61Y	ENSP00000340944:D61Y	D	+	1	0	PTPN11	111372548	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.860000	0.99555	2.798000	0.96311	0.650000	0.86243	GAT		0.423	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2		
PTPN11	5781	hgsc.bcm.edu	37	12	112888197	112888197	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:112888197T>C	ENST00000351677.2	+	3	411	c.213T>C	c.(211-213)ttT>ttC	p.F71F	PTPN11_ENST00000392597.1_Silent_p.F71F	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	71	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.		F -> K (in acute myeloid leukemia; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12717436}.|F -> L (in myelodysplastic syndrome). {ECO:0000269|PubMed:12634870, ECO:0000269|PubMed:12717436}.		abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.F71L(5)|p.F71K(1)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						GGGAGAAATTTGCCACTTTGG	0.418			Mis		"""JMML, AML, MDS"""		Noonan Syndrome		Noonan syndrome																															Dom	yes		12	12q24.1	5781	"""protein tyrosine phosphatase, non-receptor type 11"""	yes	L	6	Substitution - Missense(6)	haematopoietic_and_lymphoid_tissue(6)	12											154.0	142.0	146.0					12																	112888197		2203	4300	6503	111372580	SO:0001819	synonymous_variant	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"", ""SH2 domain containing"""	9644	protein-coding gene	gene with protein product		176876	"""Noonan syndrome 1"""	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.213T>C	12.37:g.112888197T>C			111372580	A8K1D9|Q96HD7	Silent	SNP	ENST00000351677.2	37	CCDS9163.1																																																																																				0.418	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2		
ACADS	35	hgsc.bcm.edu	37	12	121176678	121176678	+	Missense_Mutation	SNP	G	G	A	rs199633532		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:121176678G>A	ENST00000242592.4	+	8	1140	c.989G>A	c.(988-990)cGc>cAc	p.R330H	RP11-173P15.7_ENST00000542620.1_RNA|ACADS_ENST00000411593.2_Missense_Mutation_p.R326H	NM_000017.2	NP_000008.1	P16219	ACADS_HUMAN	acyl-CoA dehydrogenase, C-2 to C-3 short chain	330					butyrate catabolic process (GO:0046359)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|protein homotetramerization (GO:0051289)|response to glucocorticoid (GO:0051384)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|butyryl-CoA dehydrogenase activity (GO:0004085)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)	p.R330H(2)		central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(3)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)	Lung NSC(355;0.163)			Flavin adenine dinucleotide(DB03147)	CTGACCTGGCGCGCTGCCATG	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		17348	0.0		0.001	False		,,,				2504	0.0																2	Substitution - Missense(2)	prostate(1)|kidney(1)	12	GRCh37	CM067634	ACADS	M							46.0	52.0	50.0					12																	121176678		2203	4300	6503	119661061	SO:0001583	missense	35			M26393	CCDS9207.1	12q24.31	2012-07-13	2010-04-30		ENSG00000122971	ENSG00000122971	1.3.8.1		90	protein-coding gene	gene with protein product		606885	"""acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain"""			2565344	Standard	NM_000017		Approved	SCAD, ACAD3	uc001tza.4	P16219	OTTHUMG00000169203	ENST00000242592.4:c.989G>A	12.37:g.121176678G>A	ENSP00000242592:p.Arg330His		119661061	P78331	Missense_Mutation	SNP	ENST00000242592.4	37	CCDS9207.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.357217	0.82243	.	.	ENSG00000122971	ENST00000242592;ENST00000411593	D;D	0.96619	-4.07;-4.07	4.63	4.63	0.57726	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.053187	0.64402	D	0.000001	D	0.96694	0.8921	L	0.33792	1.035	0.58432	D	0.999993	D;P;P	0.89917	1.0;0.737;0.737	D;B;B	0.80764	0.994;0.14;0.14	D	0.97682	1.0173	10	0.62326	D	0.03	.	17.5068	0.87748	0.0:0.0:1.0:0.0	.	326;330;330	E9PE82;E5KSD5;P16219	.;.;ACADS_HUMAN	H	330;326	ENSP00000242592:R330H;ENSP00000401045:R326H	ENSP00000242592:R330H	R	+	2	0	ACADS	119661061	1.000000	0.71417	0.916000	0.36221	0.916000	0.54674	7.185000	0.77714	2.125000	0.65367	0.561000	0.74099	CGC		0.642	ACADS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402861.1	NM_000017	
CAMKK2	10645	hgsc.bcm.edu	37	12	121707359	121707359	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:121707359G>A	ENST00000324774.5	-	4	1373	c.545C>T	c.(544-546)gCc>gTc	p.A182V	CAMKK2_ENST00000535524.1_Intron|CAMKK2_ENST00000347034.2_Missense_Mutation_p.A182V|CAMKK2_ENST00000402834.4_Missense_Mutation_p.A182V|CAMKK2_ENST00000392474.2_Missense_Mutation_p.A182V|CAMKK2_ENST00000412367.2_Missense_Mutation_p.A182V|CAMKK2_ENST00000538733.1_Missense_Mutation_p.A182V|CAMKK2_ENST00000446440.2_Missense_Mutation_p.A182V|CAMKK2_ENST00000337174.3_Missense_Mutation_p.A182V|CAMKK2_ENST00000392473.2_Missense_Mutation_p.A182V|CAMKK2_ENST00000404169.3_Missense_Mutation_p.A182V	NM_006549.3	NP_006540.3	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase kinase 2, beta	182	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> T (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		calcium-mediated signaling (GO:0019722)|MAPK cascade (GO:0000165)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TTCATTGTAGGCCAACTTGAC	0.468																																																	0			12											168.0	143.0	151.0					12																	121707359		2203	4300	6503	120191742	SO:0001583	missense	10645			AF101264	CCDS9216.1, CCDS9217.1, CCDS9218.1, CCDS9219.1, CCDS44999.1, CCDS53837.1, CCDS58283.1	12q24.2	2002-08-13				ENSG00000110931			1470	protein-coding gene	gene with protein product		615002				9662074	Standard	NM_172226		Approved	CAMKK, KIAA0787, CAMKKB, MGC15254	uc001tzu.3	Q96RR4		ENST00000324774.5:c.545C>T	12.37:g.121707359G>A	ENSP00000312741:p.Ala182Val		120191742	A8K7Q7|O94883|Q8IUG2|Q8IUG3|Q8N3I4|Q8WY03|Q8WY04|Q8WY05|Q8WY06|Q96RP1|Q96RP2|Q96RR3|Q9BWE9|Q9UER3|Q9UES2|Q9Y5N2	Missense_Mutation	SNP	ENST00000324774.5	37	CCDS9216.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.976640	0.92982	.	.	ENSG00000110931	ENST00000392474;ENST00000347034;ENST00000538733;ENST00000337174;ENST00000324774;ENST00000412367;ENST00000404169;ENST00000360452;ENST00000446440;ENST00000392473	T;T;T;T;T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56	4.69	4.69	0.59074	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.51041	0.1651	N	0.13198	0.31	0.80722	D	1	P;P;P;B;P;P;P	0.50710	0.778;0.907;0.808;0.421;0.924;0.938;0.808	P;P;P;B;P;P;P	0.55303	0.55;0.664;0.664;0.421;0.664;0.773;0.54	T	0.55231	-0.8173	10	0.45353	T	0.12	0.1016	17.5005	0.87730	0.0:0.0:1.0:0.0	.	182;182;182;182;182;182;182	Q96RR4-6;Q96RR4-2;Q96RR4-7;Q96RR4-5;Q96RR4-4;Q96RR4;Q96RR4-3	.;.;.;.;.;KKCC2_HUMAN;.	V	182;182;182;182;182;182;182;165;182;182	ENSP00000376266:A182V;ENSP00000321230:A182V;ENSP00000445944:A182V;ENSP00000336634:A182V;ENSP00000312741:A182V;ENSP00000388368:A182V;ENSP00000384600:A182V;ENSP00000388273:A182V;ENSP00000376265:A182V	ENSP00000312741:A182V	A	-	2	0	CAMKK2	120191742	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.709000	0.91379	2.560000	0.86352	0.655000	0.94253	GCC		0.468	CAMKK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402563.1	NM_172226	
RSRC2	65117	hgsc.bcm.edu	37	12	123006784	123006784	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:123006784T>C	ENST00000331738.7	-	2	214	c.69A>G	c.(67-69)aaA>aaG	p.K23K	RSRC2_ENST00000354654.2_5'UTR	NM_023012.5	NP_075388.2	Q7L4I2	RSRC2_HUMAN	arginine/serine-rich coiled-coil 2	23							poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|urinary_tract(2)	24	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.14e-05)|Epithelial(86;0.000183)|BRCA - Breast invasive adenocarcinoma(302;0.201)		ACTGCTCTTTTTTCTTATCTC	0.353																																																	0			12											157.0	145.0	149.0					12																	123006784		2203	4300	6503	121572737	SO:0001819	synonymous_variant	65117			AF161432	CCDS31920.1	12q24.31	2007-02-13			ENSG00000111011	ENSG00000111011			30559	protein-coding gene	gene with protein product						17203224	Standard	NM_023012		Approved	FLJ11021	uc001ucr.3	Q7L4I2	OTTHUMG00000167572	ENST00000331738.7:c.69A>G	12.37:g.123006784T>C			121572737	Q6N040|Q6NW16|Q9H864	Silent	SNP	ENST00000331738.7	37	CCDS31920.1																																																																																				0.353	RSRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395096.3	NM_023012	
HIP1R	9026	hgsc.bcm.edu	37	12	123340853	123340853	+	Missense_Mutation	SNP	A	A	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:123340853A>T	ENST00000253083.4	+	15	1488	c.1363A>T	c.(1363-1365)Agt>Tgt	p.S455C		NM_003959.1	NP_003950.1	O75146	HIP1R_HUMAN	huntingtin interacting protein 1 related	455					receptor-mediated endocytosis (GO:0006898)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(5)|kidney(6)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	26	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)		GGAAAAGCACAGTGAGCTCGT	0.662																																																	0			12											112.0	104.0	107.0					12																	123340853		2203	4300	6503	121906806	SO:0001583	missense	9026			AB013384	CCDS31922.1	12q24	2007-12-07			ENSG00000130787	ENSG00000130787			18415	protein-coding gene	gene with protein product		605613				16415883	Standard	NM_003959		Approved	KIAA0655, HIP3, HIP12, FLJ14000, ILWEQ	uc001udj.1	O75146	OTTHUMG00000168765	ENST00000253083.4:c.1363A>T	12.37:g.123340853A>T	ENSP00000253083:p.Ser455Cys		121906806	A6NHQ6|Q6NXG8|Q9UED9	Missense_Mutation	SNP	ENST00000253083.4	37	CCDS31922.1	.	.	.	.	.	.	.	.	.	.	A	16.14	3.039991	0.55003	.	.	ENSG00000130787	ENST00000253083	T	0.16897	2.31	4.84	2.49	0.30216	.	0.228496	0.52532	D	0.000075	T	0.26738	0.0654	M	0.71581	2.175	0.33198	D	0.551805	D;D;D	0.58620	0.967;0.967;0.983	P;P;P	0.51266	0.642;0.664;0.599	T	0.41752	-0.9491	10	0.87932	D	0	-4.7583	8.704	0.34343	0.8442:0.0:0.1558:0.0	.	455;455;443	O75146;Q6NXG8;B3KQW8	HIP1R_HUMAN;.;.	C	455	ENSP00000253083:S455C	ENSP00000253083:S455C	S	+	1	0	HIP1R	121906806	1.000000	0.71417	0.889000	0.34880	0.471000	0.32888	3.539000	0.53604	0.239000	0.21243	0.459000	0.35465	AGT		0.662	HIP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400935.1	NM_003959	
SETD8	387893	hgsc.bcm.edu	37	12	123892040	123892040	+	Splice_Site	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:123892040C>T	ENST00000402868.3	+	8	1275	c.849C>T	c.(847-849)tgC>tgT	p.C283C	SETD8_ENST00000330479.4_Splice_Site_p.C283C			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	324	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		TCCCCTCCAGCGTGGATGCAA	0.498																																																	0			12											70.0	56.0	60.0					12																	123892040		2203	4300	6503	122457993	SO:0001630	splice_region_variant	387893			AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955		"""Chromatin-modifying enzymes / K-methyltransferases"""	29489	protein-coding gene	gene with protein product		607240				15933070, 12086618, 12121615	Standard	NM_020382		Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.849-1C>T	12.37:g.123892040C>T			122457993	A8K9D0|Q86W83|Q8TD09	Silent	SNP	ENST00000402868.3	37	CCDS9247.1																																																																																				0.498	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318263.1	NM_020382	Silent
DNAH10	196385	hgsc.bcm.edu	37	12	124352061	124352061	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:124352061T>C	ENST00000409039.3	+	41	6886	c.6861T>C	c.(6859-6861)taT>taC	p.Y2287Y		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2287	AAA 2. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		ATGTGCCCTATCTCATGGATG	0.368																																																	0			12											88.0	82.0	84.0					12																	124352061		1876	4098	5974	122918014	SO:0001819	synonymous_variant	196385			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.6861T>C	12.37:g.124352061T>C			122918014	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																				0.368	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
TMEM132B	114795	hgsc.bcm.edu	37	12	125834441	125834441	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:125834441G>A	ENST00000299308.3	+	2	504	c.496G>A	c.(496-498)Gag>Aag	p.E166K	TMEM132B_ENST00000418253.2_3'UTR	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	166						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		TGCTTTCCCTGAGGCCAGGGA	0.587																																																	0			12											83.0	85.0	84.0					12																	125834441		2002	4195	6197	124400394	SO:0001583	missense	114795			AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.496G>A	12.37:g.125834441G>A	ENSP00000299308:p.Glu166Lys		124400394	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	37	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	G	35	5.447518	0.96205	.	.	ENSG00000139364	ENST00000299308	T	0.14391	2.51	5.34	5.34	0.76211	.	.	.	.	.	T	0.36744	0.0978	M	0.69523	2.12	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.05209	-1.0899	9	0.19147	T	0.46	.	19.0585	0.93076	0.0:0.0:1.0:0.0	.	166	Q14DG7	T132B_HUMAN	K	166	ENSP00000299308:E166K	ENSP00000299308:E166K	E	+	1	0	TMEM132B	124400394	1.000000	0.71417	0.950000	0.38849	0.956000	0.61745	9.540000	0.98080	2.488000	0.83962	0.655000	0.94253	GAG		0.587	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907	
OR4N4	283694	hgsc.bcm.edu	37	15	22383320	22383320	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:22383320A>G	ENST00000328795.4	+	1	939	c.848A>G	c.(847-849)aAt>aGt	p.N283S	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	283						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N283I(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(19)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	40		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		CCATTGATGAATCCTATGATT	0.403																																																	1	Substitution - Missense(1)	ovary(1)	15											135.0	123.0	127.0					15																	22383320		2188	4259	6447	19884684	SO:0001583	missense	283694			AI018459	CCDS32173.1	15q11.2	2012-08-09				ENSG00000183706		"""GPCR / Class A : Olfactory receptors"""	15375	protein-coding gene	gene with protein product							Standard	NM_001005241		Approved		uc010tzv.2	Q8N0Y3		ENST00000328795.4:c.848A>G	15.37:g.22383320A>G	ENSP00000332500:p.Asn283Ser		19884684	Q6IEY3|Q6IF56	Missense_Mutation	SNP	ENST00000328795.4	37	CCDS32173.1	.	.	.	.	.	.	.	.	.	.	.	13.68	2.309110	0.40895	.	.	ENSG00000183706	ENST00000328795	T	0.58652	0.32	3.2	3.2	0.36748	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000117	T	0.61489	0.2351	L	0.60957	1.885	0.34131	D	0.665298	P	0.47350	0.894	P	0.51866	0.682	T	0.74022	-0.3798	10	0.87932	D	0	-4.4181	9.7407	0.40416	1.0:0.0:0.0:0.0	.	283	Q8N0Y3	OR4N4_HUMAN	S	283	ENSP00000332500:N283S	ENSP00000332500:N283S	N	+	2	0	OR4N4	19884684	1.000000	0.71417	1.000000	0.80357	0.190000	0.23558	8.318000	0.89990	1.454000	0.47793	0.332000	0.21555	AAT		0.403	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1		
GABRA5	2558	hgsc.bcm.edu	37	15	27188386	27188386	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:27188386C>T	ENST00000335625.5	+	10	1790	c.902C>T	c.(901-903)aCg>aTg	p.T301M	GABRA5_ENST00000355395.5_Missense_Mutation_p.T301M|GABRA5_ENST00000400081.3_Missense_Mutation_p.T301M	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	301					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	CTGACCATGACGACCCTCAGC	0.612																																																	0			15											16.0	17.0	17.0					15																	27188386		2091	4208	6299	24771132	SO:0001583	missense	2558				CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4079	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 5"""	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.902C>T	15.37:g.27188386C>T	ENSP00000335592:p.Thr301Met		24771132	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Missense_Mutation	SNP	ENST00000335625.5	37	CCDS45194.1	.	.	.	.	.	.	.	.	.	.	-	24.3	4.513029	0.85389	.	.	ENSG00000186297	ENST00000335625;ENST00000355395;ENST00000400081	D;D;D	0.93811	-3.29;-3.29;-3.29	5.27	4.36	0.52297	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.046170	0.85682	D	0.000000	D	0.96093	0.8727	M	0.75150	2.29	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96360	0.9265	10	0.87932	D	0	.	13.2941	0.60286	0.0:0.9235:0.0:0.0765	.	301	P31644	GBRA5_HUMAN	M	301	ENSP00000335592:T301M;ENSP00000347557:T301M;ENSP00000382953:T301M	ENSP00000335592:T301M	T	+	2	0	GABRA5	24771132	1.000000	0.71417	0.946000	0.38457	0.996000	0.88848	7.600000	0.82769	1.359000	0.45940	0.651000	0.88453	ACG		0.612	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1		
SEMA6D	80031	hgsc.bcm.edu	37	15	48058183	48058183	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:48058183T>C	ENST00000316364.5	+	14	1984	c.1545T>C	c.(1543-1545)tgT>tgC	p.C515C	SEMA6D_ENST00000354744.4_Silent_p.C515C|SEMA6D_ENST00000558014.1_Silent_p.C515C|SEMA6D_ENST00000355997.3_Silent_p.C515C|SEMA6D_ENST00000558816.1_Silent_p.C515C|SEMA6D_ENST00000389433.2_Silent_p.C515C|SEMA6D_ENST00000537942.1_Silent_p.C515C|SEMA6D_ENST00000389428.3_Silent_p.C515C|SEMA6D_ENST00000389432.2_Silent_p.C515C|SEMA6D_ENST00000358066.4_Silent_p.C515C|SEMA6D_ENST00000536845.2_Silent_p.C515C	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	515	PSI.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		TCAGTCGCTGTGAGCGTTATG	0.418																																																	0			15											229.0	210.0	217.0					15																	48058183		2198	4297	6495	45845475	SO:0001819	synonymous_variant	80031			AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"""Semaphorins"""	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.1545T>C	15.37:g.48058183T>C			45845475	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Silent	SNP	ENST00000316364.5	37	CCDS32225.1																																																																																				0.418	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966	
COPS2	9318	hgsc.bcm.edu	37	15	49426216	49426216	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:49426216C>T	ENST00000388901.5	-	8	878	c.805G>A	c.(805-807)Gga>Aga	p.G269R	COPS2_ENST00000542928.1_Missense_Mutation_p.G205R|COPS2_ENST00000299259.6_Missense_Mutation_p.G276R	NM_001143887.1|NM_004236.3	NP_001137359.1|NP_004227.1	P61201	CSN2_HUMAN	COP9 signalosome subunit 2	269	PCI.				cell proliferation (GO:0008283)|cullin deneddylation (GO:0010388)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(2)	18		all_lung(180;0.0428)		all cancers(107;1.34e-07)|GBM - Glioblastoma multiforme(94;3.02e-05)		CTTGGACTTCCAGATTCATCA	0.373																																					NSCLC(36;322 1063 10349 30082 48062)|Esophageal Squamous(122;685 1633 15569 21293 52803)												0			15											94.0	101.0	98.0					15																	49426216		2196	4295	6491	47213508	SO:0001583	missense	9318			AF212227	CCDS32235.1, CCDS45257.1	15q21.2	2013-03-14	2013-03-14						30747	protein-coding gene	gene with protein product		604508	"""COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis)"""			7776974, 9535219	Standard	NM_004236		Approved	TRIP15, ALIEN, CSN2	uc001zxh.3	P61201		ENST00000388901.5:c.805G>A	15.37:g.49426216C>T	ENSP00000373553:p.Gly269Arg		47213508	O88950|Q15647|Q6FGP4|Q9BY54|Q9R249|Q9UNI2|Q9UNQ5	Missense_Mutation	SNP	ENST00000388901.5	37	CCDS32235.1	.	.	.	.	.	.	.	.	.	.	C	35	5.475641	0.96291	.	.	ENSG00000166200	ENST00000299259;ENST00000388901;ENST00000542928	T;T;T	0.75260	2.25;-0.92;2.25	5.93	5.93	0.95920	Tetratricopeptide-like helical (1);PCI/PINT associated module (1);	0.000000	0.85682	D	0.000000	D	0.89622	0.6768	M	0.90019	3.08	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.90636	0.4571	10	0.87932	D	0	-0.0025	20.3465	0.98790	0.0:1.0:0.0:0.0	.	205;277;269	B4DIH5;Q59EL2;P61201	.;.;CSN2_HUMAN	R	276;269;205	ENSP00000299259:G276R;ENSP00000373553:G269R;ENSP00000443664:G205R	ENSP00000299259:G276R	G	-	1	0	COPS2	47213508	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.818000	0.86416	2.798000	0.96311	0.655000	0.94253	GGA		0.373	COPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417840.1	NM_004236	
STRA6	64220	hgsc.bcm.edu	37	15	74494576	74494576	+	Silent	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:74494576G>A	ENST00000323940.5	-	2	278	c.33C>T	c.(31-33)tcC>tcT	p.S11S	RP11-60L3.1_ENST00000561332.1_RNA|RP11-60L3.1_ENST00000560148.1_RNA|STRA6_ENST00000432245.2_Silent_p.S11S|STRA6_ENST00000423167.2_Silent_p.S11S|STRA6_ENST00000395105.4_Silent_p.S11S|STRA6_ENST00000563965.1_Silent_p.S50S|STRA6_ENST00000574278.1_Silent_p.S26S|RP11-60L3.1_ENST00000558645.1_RNA|STRA6_ENST00000449139.2_Silent_p.S11S|STRA6_ENST00000535552.1_Silent_p.S48S|STRA6_ENST00000416286.3_Silent_p.S11S|STRA6_ENST00000574439.1_5'UTR	NM_001142617.1|NM_001142618.1|NM_001142619.1	NP_001136089.1|NP_001136090.1|NP_001136091.1	Q9BX79	STRA6_HUMAN	stimulated by retinoic acid 6	11					adrenal gland development (GO:0030325)|alveolar primary septum development (GO:0061143)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|cognition (GO:0050890)|developmental growth (GO:0048589)|diaphragm development (GO:0060539)|digestive tract morphogenesis (GO:0048546)|ductus arteriosus closure (GO:0097070)|ear development (GO:0043583)|embryonic camera-type eye formation (GO:0060900)|embryonic digestive tract development (GO:0048566)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|feeding behavior (GO:0007631)|female genitalia development (GO:0030540)|head development (GO:0060322)|head morphogenesis (GO:0060323)|heart development (GO:0007507)|kidney development (GO:0001822)|learning (GO:0007612)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung vasculature development (GO:0060426)|neuromuscular process (GO:0050905)|nose morphogenesis (GO:0043585)|paramesonephric duct development (GO:0061205)|phototransduction, visible light (GO:0007603)|positive regulation of behavior (GO:0048520)|positive regulation of JAK-STAT cascade (GO:0046427)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol transport (GO:0034633)|smooth muscle tissue development (GO:0048745)|uterus morphogenesis (GO:0061038)|ventricular septum development (GO:0003281)|vitamin A import (GO:0071939)|vocal learning (GO:0042297)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	receptor activity (GO:0004872)|vitamin transporter activity (GO:0051183)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|skin(1)|stomach(2)	26						TGGCCCCGGGGGAGGTCTGGT	0.592																																																	0			15											56.0	56.0	56.0					15																	74494576		2198	4297	6495	72281629	SO:0001819	synonymous_variant	64220			AF352728	CCDS10261.1, CCDS45301.1, CCDS45302.1, CCDS55973.1, CCDS55974.1, CCDS58387.1	15q24.1	2014-07-14	2012-12-07		ENSG00000137868	ENSG00000137868			30650	protein-coding gene	gene with protein product	"""retinol binding protein 4 receptor"""	610745	"""stimulated by retinoic acid gene 6 homolog (mouse)"", ""stimulated by retinoic acid 6 homolog (mouse)"""			17255476, 17273977	Standard	NM_022369		Approved	FLJ12541	uc002axj.3	Q9BX79	OTTHUMG00000138998	ENST00000323940.5:c.33C>T	15.37:g.74494576G>A			72281629	A8K7F1|B7Z5M9|B7Z862|D3DW54|F5GYI8|I3L1G8|Q6PJF8|Q71RB9|Q7L9G1|Q7Z3U9|Q8TB21|Q9BX78|Q9H9U8	Silent	SNP	ENST00000323940.5	37	CCDS10261.1																																																																																				0.592	STRA6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272891.1		
STARD5	80765	hgsc.bcm.edu	37	15	81605707	81605707	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:81605707T>C	ENST00000302824.6	-	6	557	c.532A>G	c.(532-534)Acc>Gcc	p.T178A		NM_181900.2	NP_871629.1	Q9NSY2	STAR5_HUMAN	StAR-related lipid transfer (START) domain containing 5	178	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				C21-steroid hormone biosynthetic process (GO:0006700)|lipid transport (GO:0006869)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytosol (GO:0005829)	lipid binding (GO:0008289)			large_intestine(3)|ovary(1)|skin(1)|stomach(1)	6						CTGAGGTCGGTATGGAAGAAT	0.552																																																	0			15											192.0	164.0	173.0					15																	81605707		2203	4300	6503	79392762	SO:0001583	missense	80765			AF480304	CCDS10318.1	15q26	2011-09-12	2007-08-16		ENSG00000172345	ENSG00000172345		"""StAR-related lipid transfer (START) domain containing"""	18065	protein-coding gene	gene with protein product		607050	"""START domain containing 5"""			12011452	Standard	NM_181900		Approved	MGC10327	uc002bgm.3	Q9NSY2	OTTHUMG00000147342	ENST00000302824.6:c.532A>G	15.37:g.81605707T>C	ENSP00000304032:p.Thr178Ala		79392762	P59094	Missense_Mutation	SNP	ENST00000302824.6	37	CCDS10318.1	.	.	.	.	.	.	.	.	.	.	T	16.61	3.170144	0.57584	.	.	ENSG00000172345	ENST00000302824	T	0.77489	-1.1	5.07	3.91	0.45181	Lipid-binding START (3);START-like domain (1);	0.058138	0.64402	D	0.000002	D	0.85301	0.5665	M	0.84082	2.675	0.54753	D	0.999984	D	0.63046	0.992	P	0.60949	0.881	D	0.83511	0.0080	10	0.30078	T	0.28	-0.3983	11.2931	0.49263	0.1368:0.0:0.0:0.8632	.	178	Q9NSY2	STAR5_HUMAN	A	178	ENSP00000304032:T178A	ENSP00000304032:T178A	T	-	1	0	STARD5	79392762	1.000000	0.71417	0.992000	0.48379	0.058000	0.15608	5.177000	0.65032	0.833000	0.34828	0.459000	0.35465	ACC		0.552	STARD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303950.2		
BNC1	646	hgsc.bcm.edu	37	15	83932792	83932792	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:83932792C>T	ENST00000345382.2	-	4	1296	c.1211G>A	c.(1210-1212)cGc>cAc	p.R404H	RP11-382A20.4_ENST00000565495.1_RNA|BNC1_ENST00000569704.1_Missense_Mutation_p.R397H	NM_001717.3	NP_001708.3	Q01954	BNC1_HUMAN	basonuclin 1	404					chromosome organization (GO:0051276)|epidermis development (GO:0008544)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R404H(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	56						GGCGCTATGGCGATTCCGGCT	0.527																																																	1	Substitution - Missense(1)	ovary(1)	15											170.0	159.0	163.0					15																	83932792		2203	4300	6503	81723796	SO:0001583	missense	646			L03427	CCDS10324.1, CCDS73771.1	15q25.1	2013-05-20	2004-04-30	2004-05-04	ENSG00000169594	ENSG00000169594		"""Zinc fingers, C2H2-type"""	1081	protein-coding gene	gene with protein product		601930	"""basonuclin"""	BNC		1332044	Standard	NM_001717		Approved	HsT19447	uc002bjt.1	Q01954	OTTHUMG00000147362	ENST00000345382.2:c.1211G>A	15.37:g.83932792C>T	ENSP00000307041:p.Arg404His		81723796	Q15840	Missense_Mutation	SNP	ENST00000345382.2	37	CCDS10324.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.745100	0.89663	.	.	ENSG00000169594	ENST00000345382;ENST00000541809	T	0.30981	1.51	5.51	5.51	0.81932	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.61022	0.2314	M	0.81341	2.54	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.65261	-0.6211	10	0.87932	D	0	-33.1899	19.4213	0.94723	0.0:1.0:0.0:0.0	.	397;404	F5GY04;Q01954	.;BNC1_HUMAN	H	404;397	ENSP00000307041:R404H	ENSP00000307041:R404H	R	-	2	0	BNC1	81723796	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.755000	0.85180	2.589000	0.87451	0.655000	0.94253	CGC		0.527	BNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304006.1	NM_001717	
PCSK6	5046	hgsc.bcm.edu	37	15	101938708	101938708	+	Silent	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:101938708G>A	ENST00000348070.1	-	8	893	c.894C>T	c.(892-894)atC>atT	p.I298I	PCSK6_ENST00000344273.2_Silent_p.I298I|PCSK6_ENST00000561177.1_5'UTR|PCSK6_ENST00000331826.7_Silent_p.I133I|PCSK6_ENST00000398181.2_Silent_p.I298I|PCSK6_ENST00000358417.3_Silent_p.I298I	NM_002570.3|NM_138320.1	NP_002561.1|NP_612193.1	P29122	PCSK6_HUMAN	proprotein convertase subtilisin/kexin type 6	299	Peptidase S8.				determination of left/right symmetry (GO:0007368)|glycoprotein metabolic process (GO:0009100)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|regulation of BMP signaling pathway (GO:0030510)|secretion by cell (GO:0032940)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|nerve growth factor binding (GO:0048406)|serine-type endopeptidase activity (GO:0004252)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TGTAAATGTCGATGTAGTTGG	0.597																																																	0			15											85.0	91.0	89.0					15																	101938708		2091	4250	6341	99756231	SO:0001819	synonymous_variant	5046				CCDS73789.1, CCDS73790.1, CCDS73791.1, CCDS73792.1, CCDS73793.1	15q26	2008-07-18	2004-06-14	2004-06-16		ENSG00000140479			8569	protein-coding gene	gene with protein product	"""subtilisin-like protease"", ""subtilisin-like proprotein convertase 4"", ""subtilisin/kexin-like protease PACE4"""	167405	"""paired basic amino acid cleaving system 4"""	PACE4		1741956	Standard	NM_002570		Approved	SPC4	uc002bwy.3	P29122		ENST00000348070.1:c.894C>T	15.37:g.101938708G>A			99756231	Q15099|Q15100|Q9UEG7|Q9UEJ1|Q9UEJ2|Q9UEJ7|Q9UEJ8|Q9UEJ9|Q9Y4G9|Q9Y4H0|Q9Y4H1	Nonsense_Mutation	SNP	ENST00000348070.1	37																																																																																					0.597	PCSK6-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_002570	
FRMPD4	9758	hgsc.bcm.edu	37	X	12712556	12712556	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:12712556G>A	ENST00000380682.1	+	9	1422	c.916G>A	c.(916-918)Gag>Aag	p.E306K		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	306	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						AGTTGCTTTCGAGTATCTCTA	0.388																																																	0			X											114.0	96.0	102.0					X																	12712556		2203	4300	6503	12622477	SO:0001583	missense	9758			AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"""PDZ domain containing 10"""	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.916G>A	X.37:g.12712556G>A	ENSP00000370057:p.Glu306Lys		12622477	A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	37	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.031547	0.93575	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.78816	-1.21	5.02	5.02	0.67125	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.000000	0.85682	D	0.000000	D	0.87625	0.6224	M	0.73217	2.22	0.52501	D	0.999952	D;D	0.89917	1.0;0.995	D;P	0.83275	0.996;0.739	D	0.89078	0.3474	10	0.72032	D	0.01	.	17.7822	0.88527	0.0:0.0:1.0:0.0	.	298;306	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	K	306;297;295	ENSP00000370057:E306K	ENSP00000304583:E295K	E	+	1	0	FRMPD4	12622477	1.000000	0.71417	0.970000	0.41538	0.979000	0.70002	9.322000	0.96357	2.217000	0.71921	0.513000	0.50165	GAG		0.388	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712	
FRMPD4	9758	hgsc.bcm.edu	37	X	12734595	12734595	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:12734595A>G	ENST00000380682.1	+	15	2523	c.2017A>G	c.(2017-2019)Acg>Gcg	p.T673A		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	673					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						TGGCTATGAAACGCTACTAGA	0.483																																																	0			X											153.0	165.0	161.0					X																	12734595		2203	4300	6503	12644516	SO:0001583	missense	9758			AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"""PDZ domain containing 10"""	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.2017A>G	X.37:g.12734595A>G	ENSP00000370057:p.Thr673Ala		12644516	A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	37	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	A	12.42	1.931377	0.34096	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.28454	1.61	5.86	0.241	0.15494	.	0.047976	0.85682	D	0.000000	T	0.12050	0.0293	N	0.08118	0	0.20975	N	0.999818	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31668	-0.9935	10	0.13853	T	0.58	-25.4542	8.0093	0.30344	0.5427:0.3871:0.0701:0.0	.	665;673	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	A	673;664;662	ENSP00000370057:T673A	ENSP00000304583:T662A	T	+	1	0	FRMPD4	12644516	1.000000	0.71417	0.012000	0.15200	0.576000	0.36127	3.275000	0.51639	-0.006000	0.14370	0.486000	0.48141	ACG		0.483	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712	
TLR8	51311	hgsc.bcm.edu	37	X	12937997	12937997	+	Missense_Mutation	SNP	C	C	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:12937997C>A	ENST00000218032.6	+	2	925	c.838C>A	c.(838-840)Cgt>Agt	p.R280S	TLR8_ENST00000311912.5_Missense_Mutation_p.R298S	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	280					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	TAATATAGATCGTTTTGCTTT	0.408																																																	0			X											109.0	90.0	97.0					X																	12937997		2203	4299	6502	12847918	SO:0001583	missense	51311			AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.838C>A	X.37:g.12937997C>A	ENSP00000218032:p.Arg280Ser		12847918	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	37	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	C	0.624	-0.820042	0.02755	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.56941	0.43;0.43	5.03	2.18	0.27775	.	0.586022	0.14193	N	0.335229	T	0.28732	0.0712	N	0.12637	0.245	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16188	-1.0411	10	0.27082	T	0.32	.	4.6572	0.12624	0.2682:0.5243:0.1278:0.0797	.	280;298	Q9NR97;D1CS70	TLR8_HUMAN;.	S	280;298	ENSP00000218032:R280S;ENSP00000312082:R298S	ENSP00000218032:R280S	R	+	1	0	TLR8	12847918	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.355000	0.20163	0.098000	0.17522	-1.528000	0.00924	CGT		0.408	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610	
CDKL5	6792	hgsc.bcm.edu	37	X	18664127	18664127	+	Splice_Site	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:18664127A>G	ENST00000379989.3	+	20	2999	c.2714A>G	c.(2713-2715)gAc>gGc	p.D905G	CDKL5_ENST00000379996.3_Splice_Site_p.D905G|RS1_ENST00000476595.1_Intron|RS1_ENST00000379984.3_Intron	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	905					neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					cactaactagacggtggatgt	0.488																																																	0			X											140.0	112.0	122.0					X																	18664127		2203	4300	6503	18574048	SO:0001630	splice_region_variant	6792			Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"""Cyclin-dependent kinases"""	11411	protein-coding gene	gene with protein product		300203	"""serine/threonine kinase 9"""	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.2714-1A>G	X.37:g.18664127A>G			18574048	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Missense_Mutation	SNP	ENST00000379989.3	37	CCDS14186.1	.	.	.	.	.	.	.	.	.	.	A	7.988	0.752565	0.15778	.	.	ENSG00000008086	ENST00000379996;ENST00000379989	T;T	0.68624	-0.34;-0.34	1.89	0.648	0.17801	.	0.326495	0.27577	N	0.018744	T	0.28167	0.0695	N	0.01168	-0.975	0.09310	N	0.999997	B	0.10296	0.003	B	0.06405	0.002	T	0.21008	-1.0258	9	.	.	.	.	4.4178	0.11465	0.6504:0.3496:0.0:0.0	.	905	O76039	CDKL5_HUMAN	G	905	ENSP00000369332:D905G;ENSP00000369325:D905G	.	D	+	2	0	CDKL5	18574048	0.389000	0.25205	0.165000	0.22776	0.063000	0.16089	0.479000	0.22228	0.105000	0.17753	0.340000	0.21749	GAC		0.488	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159	Missense_Mutation
CXorf22	170063	hgsc.bcm.edu	37	X	35988902	35988902	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:35988902T>C	ENST00000297866.5	+	11	1898	c.1832T>C	c.(1831-1833)gTt>gCt	p.V611A		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	611										breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						TTCACAAAAGTTCCAAGATTT	0.279																																																	0			X											40.0	35.0	37.0					X																	35988902		2202	4293	6495	35898823	SO:0001583	missense	170063			BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.1832T>C	X.37:g.35988902T>C	ENSP00000297866:p.Val611Ala		35898823	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	37	CCDS14237.2	.	.	.	.	.	.	.	.	.	.	T	0.238	-1.015474	0.02078	.	.	ENSG00000165164	ENST00000297866	T	0.16597	2.33	5.0	-1.55	0.08558	.	0.728208	0.13134	N	0.411214	T	0.08492	0.0211	N	0.17474	0.49	0.09310	N	1	B	0.18310	0.027	B	0.17098	0.017	T	0.41378	-0.9512	10	0.15499	T	0.54	-27.6915	8.8496	0.35192	0.0:0.5333:0.0:0.4667	.	611	Q6ZTR5	CX022_HUMAN	A	611	ENSP00000297866:V611A	ENSP00000297866:V611A	V	+	2	0	CXorf22	35898823	0.020000	0.18652	0.173000	0.22940	0.003000	0.03518	0.120000	0.15647	-0.429000	0.07329	-0.328000	0.08392	GTT		0.279	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632	
KDM5C	8242	hgsc.bcm.edu	37	X	53223695	53223695	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:53223695A>G	ENST00000375401.3	-	23	4196	c.3664T>C	c.(3664-3666)Tct>Cct	p.S1222P	KDM5C_ENST00000375383.3_Missense_Mutation_p.S1181P|KDM5C_ENST00000452825.3_Missense_Mutation_p.S1155P|KDM5C_ENST00000404049.3_Missense_Mutation_p.S1221P|KDM5C_ENST00000375379.3_Missense_Mutation_p.S1222P	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	1222					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)	p.S1222P(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						GGCCTCGGAGAGCTGAGGAGG	0.637			"""N, F, S"""		clear cell renal carcinoma																																			Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	1	Substitution - Missense(1)	kidney(1)	X											135.0	76.0	96.0					X																	53223695		2202	4298	6500	53240420	SO:0001583	missense	8242			Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	11114	protein-coding gene	gene with protein product		314690	"""Jumonji, AT rich interactive domain 1C (RBP2-like)"", ""Smcy homolog, X-linked (mouse)"", ""jumonji, AT rich interactive domain 1C"", ""mental retardation, X-linked 13"""	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.3664T>C	X.37:g.53223695A>G	ENSP00000364550:p.Ser1222Pro		53240420	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Missense_Mutation	SNP	ENST00000375401.3	37	CCDS14351.1	.	.	.	.	.	.	.	.	.	.	a	8.723	0.914794	0.17907	.	.	ENSG00000126012	ENST00000452825;ENST00000375401;ENST00000404049;ENST00000375379;ENST00000375383	T;T;T;T;T	0.00932	5.53;5.53;5.53;5.53;5.53	4.08	4.08	0.47627	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.355088	0.26029	N	0.026761	T	0.01287	0.0042	L	0.46670	1.46	0.29529	N	0.852945	B;B;B	0.11235	0.004;0.004;0.004	B;B;B	0.15484	0.013;0.009;0.006	T	0.16958	-1.0385	10	0.49607	T	0.09	-17.0743	10.1937	0.43041	1.0:0.0:0.0:0.0	.	1155;1221;1222	F5H3T1;B0QZ44;P41229	.;.;KDM5C_HUMAN	P	1155;1222;1221;1222;1181	ENSP00000445176:S1155P;ENSP00000364550:S1222P;ENSP00000385394:S1221P;ENSP00000364528:S1222P;ENSP00000364532:S1181P	ENSP00000364528:S1222P	S	-	1	0	KDM5C	53240420	0.509000	0.26163	0.991000	0.47740	0.741000	0.42261	0.219000	0.17641	1.522000	0.49001	0.427000	0.28365	TCT		0.637	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187	
AR	367	hgsc.bcm.edu	37	X	66765185	66765185	+	Missense_Mutation	SNP	A	A	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:66765185A>T	ENST00000374690.3	+	1	721	c.197A>T	c.(196-198)cAg>cTg	p.Q66L	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q66L|AR_ENST00000504326.1_Missense_Mutation_p.Q66L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	66	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	cagcagcagcagcagcagcag	0.677									Androgen Insensitivity Syndrome																																								0			X											4.0	8.0	7.0					X																	66765185		1431	2929	4360	66681910	SO:0001583	missense	374	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"""Nuclear hormone receptors"""	644	protein-coding gene	gene with protein product	"""testicular feminization"", ""Kennedy disease"""	313700	"""dihydrotestosterone receptor"", ""spinal and bulbar muscular atrophy"""	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.197A>T	X.37:g.66765185A>T	ENSP00000363822:p.Gln66Leu		66681910	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	37	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	11.50	1.658247	0.29425	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.70986	-0.53;-0.53;-0.53	1.43	1.43	0.22495	.	2.785180	0.01967	U	0.043766	T	0.72112	0.3420	N	0.19112	0.55	0.19945	N	0.999949	P;P;P	0.49559	0.807;0.925;0.807	D;D;P	0.67900	0.932;0.954;0.728	T	0.59862	-0.7374	10	0.38643	T	0.18	.	4.8652	0.13604	1.0:0.0:0.0:0.0	.	66;66;64	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	66	ENSP00000363822:Q66L;ENSP00000421155:Q66L;ENSP00000379359:Q66L	ENSP00000363822:Q66L	Q	+	2	0	AR	66681910	0.019000	0.18553	0.911000	0.35937	0.616000	0.37450	-0.130000	0.10498	0.644000	0.30656	0.084000	0.15446	CAG		0.677	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044	
AR	367	hgsc.bcm.edu	37	X	66765188	66765188	+	Missense_Mutation	SNP	A	A	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:66765188A>T	ENST00000374690.3	+	1	724	c.200A>T	c.(199-201)cAg>cTg	p.Q67L	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q67L|AR_ENST00000504326.1_Missense_Mutation_p.Q67L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	67	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	cagcagcagcagcagcagcag	0.672									Androgen Insensitivity Syndrome																																								0			X											4.0	8.0	7.0					X																	66765188		1328	2795	4123	66681913	SO:0001583	missense	374	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"""Nuclear hormone receptors"""	644	protein-coding gene	gene with protein product	"""testicular feminization"", ""Kennedy disease"""	313700	"""dihydrotestosterone receptor"", ""spinal and bulbar muscular atrophy"""	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.200A>T	X.37:g.66765188A>T	ENSP00000363822:p.Gln67Leu		66681913	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	37	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	12.39	1.924161	0.34002	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.59224	0.28;0.28;0.28	1.43	1.43	0.22495	.	1.958740	0.03276	U	0.185421	T	0.60483	0.2272	N	0.19112	0.55	0.19945	N	0.999946	P;P;P	0.49559	0.807;0.925;0.807	D;D;P	0.65140	0.932;0.932;0.728	T	0.51325	-0.8720	10	0.72032	D	0.01	.	4.8652	0.13604	1.0:0.0:0.0:0.0	.	67;67;65	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	67	ENSP00000363822:Q67L;ENSP00000421155:Q67L;ENSP00000379359:Q67L	ENSP00000363822:Q67L	Q	+	2	0	AR	66681913	0.407000	0.25352	0.994000	0.49952	0.753000	0.42808	0.127000	0.15790	0.644000	0.30656	0.084000	0.15446	CAG		0.672	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044	
KIAA2022	340533	hgsc.bcm.edu	37	X	73959989	73959989	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:73959989T>C	ENST00000055682.6	-	3	5014	c.4403A>G	c.(4402-4404)gAg>gGg	p.E1468G		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	1468					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)	p.E1468G(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						CTGTTCTCGCTCCATGTGCTT	0.473																																																	1	Substitution - Missense(1)	ovary(1)	X											209.0	164.0	179.0					X																	73959989		2203	4300	6503	73876714	SO:0001583	missense	340533				CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"""XLMR-related protein, neurite extension"""	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.4403A>G	X.37:g.73959989T>C	ENSP00000055682:p.Glu1468Gly		73876714	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	37	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	T	19.14	3.769015	0.69992	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	T;T	0.39997	1.05;1.05	5.36	5.36	0.76844	.	0.154190	0.56097	D	0.000022	T	0.43055	0.1230	L	0.29908	0.895	0.52099	D	0.999942	D	0.53312	0.959	P	0.50659	0.647	T	0.44112	-0.9349	10	0.87932	D	0	-10.3741	14.4375	0.67293	0.0:0.0:0.0:1.0	.	1468	Q5QGS0	K2022_HUMAN	G	1468	ENSP00000362567:E1468G;ENSP00000055682:E1468G	ENSP00000055682:E1468G	E	-	2	0	KIAA2022	73876714	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.698000	0.84413	1.789000	0.52484	0.441000	0.28932	GAG		0.473	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537	
FAM46D	169966	hgsc.bcm.edu	37	X	79698170	79698170	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:79698170T>C	ENST00000308293.5	+	3	371	c.132T>C	c.(130-132)atT>atC	p.I44I	FAM46D_ENST00000538312.1_Silent_p.I44I	NM_152630.4	NP_689843.1	Q8NEK8	FA46D_HUMAN	family with sequence similarity 46, member D	44										kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23						AAGACATCATTCATGTTGTGA	0.383																																																	0			X											123.0	106.0	111.0					X																	79698170		2202	4298	6500	79584826	SO:0001819	synonymous_variant	169966			BX537938	CCDS14446.1	Xq21.1	2009-08-18			ENSG00000174016	ENSG00000174016			28399	protein-coding gene	gene with protein product	"""cancer/testis antigen 112"""					12477932	Standard	NM_152630		Approved	MGC26999, CT1.26, CT112	uc004edl.1	Q8NEK8	OTTHUMG00000021902	ENST00000308293.5:c.132T>C	X.37:g.79698170T>C			79584826	B2R9Q6|Q7Z3F6|Q8NHU1	Silent	SNP	ENST00000308293.5	37	CCDS14446.1																																																																																				0.383	FAM46D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057338.1	NM_152630	
HMGN5	79366	hgsc.bcm.edu	37	X	80370223	80370223	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:80370223T>C	ENST00000358130.2	-	7	1102	c.774A>G	c.(772-774)gaA>gaG	p.E258E	HMGN5_ENST00000491275.1_5'Flank	NM_030763.2	NP_110390.1	P82970	HMGN5_HUMAN	high mobility group nucleosome binding domain 5	258					chromatin modification (GO:0016568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	10						cttcttcctcttcttttaaat	0.343																																																	0			X											240.0	213.0	222.0					X																	80370223		1620	2844	4464	80256879	SO:0001819	synonymous_variant	0			AF250329	CCDS14448.1	Xq13.3	2011-07-01	2011-04-05	2009-09-15	ENSG00000198157	ENSG00000198157		"""High-mobility group / Canonical"""	8013	protein-coding gene	gene with protein product		300385	"""nucleosomal binding protein 1"", ""high-mobility group nucleosome binding domain 5"""	NSBP1		11161810, 19748358	Standard	NM_030763		Approved		uc004eee.1	P82970	OTTHUMG00000021911	ENST00000358130.2:c.774A>G	X.37:g.80370223T>C			80256879	Q5JSL1	Silent	SNP	ENST00000358130.2	37	CCDS14448.1																																																																																				0.343	HMGN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057354.1	NM_030763	
AGTR2	186	hgsc.bcm.edu	37	X	115304581	115304581	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:115304581C>T	ENST00000371906.4	+	3	1238	c.1048C>T	c.(1048-1050)Cgg>Tgg	p.R350W		NM_000686.4	NP_000677.2	P50052	AGTR2_HUMAN	angiotensin II receptor, type 2	350					aldosterone secretion (GO:0035932)|angiotensin-activated signaling pathway (GO:0038166)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|brain renin-angiotensin system (GO:0002035)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell surface receptor signaling pathway (GO:0007166)|cellular response to dexamethasone stimulus (GO:0071549)|cellular sodium ion homeostasis (GO:0006883)|cerebellar cortex development (GO:0021695)|dopamine biosynthetic process (GO:0042416)|exploration behavior (GO:0035640)|extracellular negative regulation of signal transduction (GO:1900116)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of heart rate (GO:0010459)|negative regulation of icosanoid secretion (GO:0032304)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of norepinephrine secretion (GO:0010700)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|regulation of blood pressure (GO:0008217)|regulation of metanephros size (GO:0035566)|regulation of systemic arterial blood pressure by circulatory renin-angiotensin (GO:0001991)|regulation of transcription factor import into nucleus (GO:0042990)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to organonitrogen compound (GO:0010243)|vasodilation by angiotensin involved in regulation of systemic arterial blood pressure (GO:0002033)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)|peptide hormone binding (GO:0017046)|receptor antagonist activity (GO:0048019)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|skin(1)	24					Tasosartan(DB01349)	TATGTCTTGCCGGAAAAGCAG	0.438																																																	0			X											93.0	87.0	89.0					X																	115304581		2203	4300	6503	115218609	SO:0001583	missense	186			AY324607	CCDS14569.1	Xq22-q23	2012-08-08			ENSG00000180772	ENSG00000180772		"""GPCR / Class A : Angiotensin receptors"""	338	protein-coding gene	gene with protein product		300034	"""angiotensin receptor 2"""			1550596	Standard	NM_000686		Approved	AT2, MRX88	uc004eqh.4	P50052	OTTHUMG00000022243	ENST00000371906.4:c.1048C>T	X.37:g.115304581C>T	ENSP00000360973:p.Arg350Trp		115218609	B2R9V1|Q13016|Q6FGY7	Missense_Mutation	SNP	ENST00000371906.4	37	CCDS14569.1	.	.	.	.	.	.	.	.	.	.	C	8.496	0.863090	0.17250	.	.	ENSG00000180772	ENST00000371906	T	0.38401	1.14	4.87	-0.991	0.10235	.	0.155918	0.40818	N	0.001015	T	0.15739	0.0379	N	0.08118	0	0.23249	N	0.998049	D	0.56968	0.978	B	0.40444	0.329	T	0.31308	-0.9948	10	0.66056	D	0.02	-4.2867	9.0441	0.36336	0.5143:0.3697:0.116:0.0	.	350	P50052	AGTR2_HUMAN	W	350	ENSP00000360973:R350W	ENSP00000360973:R350W	R	+	1	2	AGTR2	115218609	0.562000	0.26586	0.744000	0.31058	0.398000	0.30690	0.347000	0.20014	-0.146000	0.11274	0.506000	0.49869	CGG		0.438	AGTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057984.1	NM_000686	
ACTRT1	139741	hgsc.bcm.edu	37	X	127185239	127185239	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:127185239T>C	ENST00000371124.3	-	1	1143	c.947A>G	c.(946-948)aAg>aGg	p.K316R		NM_138289.3	NP_612146.1	Q8TDG2	ACTT1_HUMAN	actin-related protein T1	316						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	34						TTCCACTTCCTTCATGAGCCT	0.493																																																	0			X											127.0	92.0	104.0					X																	127185239		2203	4300	6503	127012920	SO:0001583	missense	139741			AF440739	CCDS14611.1	Xq25	2008-02-05	2005-11-22		ENSG00000123165	ENSG00000123165			24027	protein-coding gene	gene with protein product		300487				12243744	Standard	NM_138289		Approved	AIP1, KIAA0705, ARIP1, Arp-T1	uc004eum.3	Q8TDG2	OTTHUMG00000022359	ENST00000371124.3:c.947A>G	X.37:g.127185239T>C	ENSP00000360165:p.Lys316Arg		127012920	Q6X7C1|Q96L10	Missense_Mutation	SNP	ENST00000371124.3	37	CCDS14611.1	.	.	.	.	.	.	.	.	.	.	T	5.618	0.298816	0.10622	.	.	ENSG00000123165	ENST00000371124	D	0.94650	-3.48	3.58	1.08	0.20341	.	0.219866	0.32952	N	0.005457	D	0.87795	0.6267	L	0.31207	0.915	0.24556	N	0.993994	B	0.21606	0.058	B	0.24701	0.055	T	0.79037	-0.1967	10	0.87932	D	0	.	3.6252	0.08111	0.1959:0.1171:0.0:0.687	.	316	Q8TDG2	ACTT1_HUMAN	R	316	ENSP00000360165:K316R	ENSP00000360165:K316R	K	-	2	0	ACTRT1	127012920	1.000000	0.71417	0.013000	0.15412	0.018000	0.09664	5.469000	0.66749	0.107000	0.17824	-0.323000	0.08544	AAG		0.493	ACTRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058192.1	NM_138289	
MAP7D3	79649	hgsc.bcm.edu	37	X	135302951	135302951	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:135302951T>C	ENST00000316077.9	-	16	2679	c.2459A>G	c.(2458-2460)gAc>gGc	p.D820G	MAP7D3_ENST00000495432.1_5'Flank|MAP7D3_ENST00000370661.1_Missense_Mutation_p.D785G|MAP7D3_ENST00000370663.5_Missense_Mutation_p.D802G	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	820					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					TATTGAAGTGTCTTTCATGCT	0.358																																																	0			X											184.0	169.0	174.0					X																	135302951		1831	4077	5908	135130617	SO:0001583	missense	79649			AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.2459A>G	X.37:g.135302951T>C	ENSP00000318086:p.Asp820Gly		135130617	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Missense_Mutation	SNP	ENST00000316077.9	37	CCDS44004.1	.	.	.	.	.	.	.	.	.	.	T	11.36	1.614386	0.28712	.	.	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663;ENST00000370660	T;T;T;T	0.20463	2.07;3.64;3.64;2.09	3.73	3.73	0.42828	.	.	.	.	.	T	0.23289	0.0563	N	0.24115	0.695	0.09310	N	1	D;D;D;D	0.71674	0.998;0.997;0.994;0.997	P;P;P;P	0.59487	0.81;0.858;0.725;0.858	T	0.08027	-1.0742	9	0.22109	T	0.4	-14.5836	8.0072	0.30332	0.0:0.0:0.0:1.0	.	802;779;820;785	B4DWD2;Q8IWC1-2;Q8IWC1;Q8IWC1-3	.;.;MA7D3_HUMAN;.	G	785;820;802;779	ENSP00000359695:D785G;ENSP00000318086:D820G;ENSP00000359697:D802G;ENSP00000359694:D779G	ENSP00000318086:D820G	D	-	2	0	MAP7D3	135130617	0.004000	0.15560	0.022000	0.16811	0.013000	0.08279	0.427000	0.21379	1.706000	0.51276	0.430000	0.28490	GAC		0.358	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2		
NAA10	8260	hgsc.bcm.edu	37	X	153195525	153195525	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:153195525T>C	ENST00000464845.1	-	8	941	c.623A>G	c.(622-624)gAc>gGc	p.D208G	NAA10_ENST00000393710.3_5'Flank|NAA10_ENST00000393712.3_3'UTR|NAA10_ENST00000370015.4_3'UTR|NAA10_ENST00000370009.1_Missense_Mutation_p.D193G	NM_001256120.1|NM_003491.3	NP_001243049.1|NP_003482.1	P41227	NAA10_HUMAN	N(alpha)-acetyltransferase 10, NatA catalytic subunit	208					DNA packaging (GO:0006323)|internal protein amino acid acetylation (GO:0006475)|N-terminal protein amino acid acetylation (GO:0006474)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleolus (GO:0005730)|nucleus (GO:0005634)	N-acetyltransferase activity (GO:0008080)|peptide alpha-N-acetyltransferase activity (GO:0004596)			breast(1)|endometrium(3)|kidney(1)|lung(3)|ovary(1)|prostate(1)	10						GTCCTTGCTGTCCCCACCACT	0.617																																					Ovarian(94;1099 1433 38814 45882 51063)												0			X											109.0	85.0	93.0					X																	153195525		2203	4300	6503	152848719	SO:0001583	missense	0			BC000308	CCDS14737.1, CCDS59179.1	Xq28	2010-05-07	2010-01-14	2010-01-14	ENSG00000102030	ENSG00000102030	2.3.1.88	"""N(alpha)-acetyltransferase subunits"""	18704	protein-coding gene	gene with protein product		300013	"""ARD1 homolog, N-acetyltransferase (S. cerevisiae)"", ""ARD1 homolog A, N-acetyltransferase (S. cerevisiae)"""	ARD1, ARD1A		7981673, 19660095	Standard	NM_003491		Approved	DXS707, TE2	uc004fjm.2	P41227	OTTHUMG00000024225	ENST00000464845.1:c.623A>G	X.37:g.153195525T>C	ENSP00000417763:p.Asp208Gly		152848719	A6NM98	Missense_Mutation	SNP	ENST00000464845.1	37	CCDS14737.1	.	.	.	.	.	.	.	.	.	.	T	17.39	3.376822	0.61735	.	.	ENSG00000102030	ENST00000464845;ENST00000370009	T;T	0.59638	0.25;0.26	5.35	5.35	0.76521	.	0.052011	0.85682	D	0.000000	T	0.50599	0.1625	L	0.43152	1.355	0.51233	D	0.99991	B;B	0.13594	0.008;0.008	B;B	0.11329	0.005;0.006	T	0.47711	-0.9096	10	0.49607	T	0.09	-39.9726	13.3468	0.60578	0.0:0.0:0.0:1.0	.	193;208	A6NM98;P41227	.;NAA10_HUMAN	G	208;193	ENSP00000417763:D208G;ENSP00000359026:D193G	ENSP00000359026:D193G	D	-	2	0	NAA10	152848719	1.000000	0.71417	0.951000	0.38953	0.962000	0.63368	7.282000	0.78630	1.794000	0.52575	0.425000	0.28330	GAC		0.617	NAA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061108.2	NM_003491	
CRIPAK	285464	hgsc.bcm.edu	37	4	1389005	1389005	+	Missense_Mutation	SNP	T	T	C	rs71614970	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:1389005T>C	ENST00000324803.4	+	1	3666	c.706T>C	c.(706-708)Tgc>Cgc	p.C236R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	236					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CACGTGCCGATGCGGAGTGCC	0.672													t|||	859	0.171526	0.1059	0.245	5008	,	,		14444	0.0437		0.2913	False		,,,				2504	0.2168																0			4											163.0	133.0	143.0					4																	1389005		2188	4292	6480	1379005	SO:0001583	missense	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.706T>C	4.37:g.1389005T>C	ENSP00000323978:p.Cys236Arg		1379005	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	t	1.791	-0.479438	0.04383	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.18338	2.22	1.11	-2.23	0.06930	Post-SET domain (1);	.	.	.	.	T	0.06781	0.0173	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.32214	-0.9915	9	0.46703	T	0.11	.	2.6743	0.05077	0.0:0.3283:0.2597:0.412	.	236	Q8N1N5	CRPAK_HUMAN	R	236;178	ENSP00000323978:C236R	ENSP00000323978:C236R	C	+	1	0	CRIPAK	1379005	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.211000	0.09332	-0.571000	0.06014	-0.530000	0.04314	TGC		0.672	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
WHSC1	7468	hgsc.bcm.edu	37	4	1962766	1962766	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:1962766A>G	ENST00000382895.3	+	20	3691	c.3260A>G	c.(3259-3261)gAa>gGa	p.E1087G	WHSC1_ENST00000382891.5_Missense_Mutation_p.E1087G|WHSC1_ENST00000382892.2_Missense_Mutation_p.E1087G|WHSC1_ENST00000482415.2_3'UTR|WHSC1_ENST00000382888.3_Missense_Mutation_p.E435G|WHSC1_ENST00000508803.1_Missense_Mutation_p.E1087G	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	1087	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		TTCCAGGGAGAATTTGTTAAC	0.522			T	IGH@	MM																																			Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	0			4											264.0	217.0	233.0					4																	1962766		2203	4300	6503	1932564	SO:0001583	missense	7468			AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685		"""Zinc fingers, PHD-type"""	12766	protein-coding gene	gene with protein product		602952				9618163, 9787135	Standard	NM_133334		Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000382895.3:c.3260A>G	4.37:g.1962766A>G	ENSP00000372351:p.Glu1087Gly		1932564	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Missense_Mutation	SNP	ENST00000382895.3	37	CCDS33940.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.961782	0.92791	.	.	ENSG00000109685	ENST00000508803;ENST00000382891;ENST00000382892;ENST00000382895;ENST00000382888	D;D;D;D;D	0.85702	-2.02;-2.02;-2.02;-2.02;-2.02	5.51	5.51	0.81932	SET domain (3);	0.000000	0.53938	D	0.000049	D	0.91050	0.7184	M	0.63428	1.95	0.80722	D	1	B;D	0.89917	0.036;1.0	B;D	0.87578	0.054;0.998	D	0.91719	0.5387	10	0.62326	D	0.03	.	15.6239	0.76833	1.0:0.0:0.0:0.0	.	435;1087	A2A2T2;O96028	.;NSD2_HUMAN	G	1087;1087;1087;1087;435	ENSP00000423972:E1087G;ENSP00000372347:E1087G;ENSP00000372348:E1087G;ENSP00000372351:E1087G;ENSP00000372344:E435G	ENSP00000372344:E435G	E	+	2	0	WHSC1	1932564	1.000000	0.71417	0.963000	0.40424	0.966000	0.64601	9.123000	0.94387	2.105000	0.64084	0.533000	0.62120	GAA		0.522	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330	
STK32B	55351	hgsc.bcm.edu	37	4	5468461	5468461	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:5468461A>G	ENST00000282908.5	+	10	1363	c.941A>G	c.(940-942)gAg>gGg	p.E314G	STK32B_ENST00000512636.1_Missense_Mutation_p.E237G|STK32B_ENST00000508728.1_3'UTR|STK32B_ENST00000510398.1_Missense_Mutation_p.E267G	NM_018401.1	NP_060871.1			serine/threonine kinase 32B											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						CCCACATTTGAGCTTGAAGAG	0.448																																																	0			4											81.0	72.0	75.0					4																	5468461		2203	4300	6503	5519362	SO:0001583	missense	55351			AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.941A>G	4.37:g.5468461A>G	ENSP00000282908:p.Glu314Gly		5519362		Missense_Mutation	SNP	ENST00000282908.5	37	CCDS3380.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.740065	0.89573	.	.	ENSG00000152953	ENST00000282908;ENST00000512636;ENST00000510398	T;T;T	0.24908	1.83;1.83;1.83	5.17	5.17	0.71159	Protein kinase-like domain (1);	0.000000	0.42420	U	0.000712	T	0.55033	0.1895	M	0.85542	2.76	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.62666	-0.6806	10	0.72032	D	0.01	.	13.8534	0.63510	1.0:0.0:0.0:0.0	.	314	Q9NY57	ST32B_HUMAN	G	314;237;267	ENSP00000282908:E314G;ENSP00000423209:E237G;ENSP00000420984:E267G	ENSP00000282908:E314G	E	+	2	0	STK32B	5519362	1.000000	0.71417	0.997000	0.53966	0.954000	0.61252	7.923000	0.87546	1.952000	0.56665	0.472000	0.43445	GAG		0.448	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401	
CABS1	85438	hgsc.bcm.edu	37	4	71201243	71201243	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:71201243T>C	ENST00000273936.5	+	1	561	c.487T>C	c.(487-489)Tct>Cct	p.S163P		NM_033122.3	NP_149113.3	Q96KC9	CABS1_HUMAN	calcium-binding protein, spermatid-specific 1	163					spermatogenesis (GO:0007283)	mitochondrial inner membrane (GO:0005743)|motile cilium (GO:0031514)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(4)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						CTCTGAAGTCTCTGGCACACT	0.413																																																	0			4											55.0	57.0	57.0					4																	71201243		2201	4298	6499	71235832	SO:0001583	missense	85438			AF380838	CCDS3539.1	4q13.3	2013-10-11	2011-01-25	2011-01-25	ENSG00000145309	ENSG00000145309			30710	protein-coding gene	gene with protein product	"""casein-like phosphoprotein"""		"""chromosome 4 open reading frame 35"""	C4orf35		19208547, 19271754	Standard	NM_033122		Approved	NYD-SP26, FLJ32897, CLPH	uc003hff.3	Q96KC9	OTTHUMG00000129405	ENST00000273936.5:c.487T>C	4.37:g.71201243T>C	ENSP00000273936:p.Ser163Pro		71235832	B2RCB5|Q86UE0|Q96M17	Missense_Mutation	SNP	ENST00000273936.5	37	CCDS3539.1	.	.	.	.	.	.	.	.	.	.	T	15.72	2.917136	0.52546	.	.	ENSG00000145309	ENST00000273936	T	0.36878	1.23	4.16	2.95	0.34219	.	0.385300	0.19291	N	0.117890	T	0.40619	0.1124	L	0.34521	1.04	0.21064	N	0.999799	D	0.61080	0.989	D	0.63957	0.92	T	0.09185	-1.0686	10	0.40728	T	0.16	-20.455	6.9084	0.24321	0.2047:0.0:0.0:0.7953	.	163	Q96KC9	CABS1_HUMAN	P	163	ENSP00000273936:S163P	ENSP00000273936:S163P	S	+	1	0	CABS1	71235832	0.970000	0.33590	0.357000	0.25798	0.011000	0.07611	1.197000	0.32211	0.904000	0.36572	0.533000	0.62120	TCT		0.413	CABS1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251561.3	NM_033122	
CABS1	85438	hgsc.bcm.edu	37	4	71201261	71201261	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:71201261A>G	ENST00000273936.5	+	1	579	c.505A>G	c.(505-507)Agc>Ggc	p.S169G		NM_033122.3	NP_149113.3	Q96KC9	CABS1_HUMAN	calcium-binding protein, spermatid-specific 1	169					spermatogenesis (GO:0007283)	mitochondrial inner membrane (GO:0005743)|motile cilium (GO:0031514)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(4)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						ACTAAAGGACAGCAGTGCTGG	0.443																																																	0			4											54.0	57.0	56.0					4																	71201261		2197	4299	6496	71235850	SO:0001583	missense	85438			AF380838	CCDS3539.1	4q13.3	2013-10-11	2011-01-25	2011-01-25	ENSG00000145309	ENSG00000145309			30710	protein-coding gene	gene with protein product	"""casein-like phosphoprotein"""		"""chromosome 4 open reading frame 35"""	C4orf35		19208547, 19271754	Standard	NM_033122		Approved	NYD-SP26, FLJ32897, CLPH	uc003hff.3	Q96KC9	OTTHUMG00000129405	ENST00000273936.5:c.505A>G	4.37:g.71201261A>G	ENSP00000273936:p.Ser169Gly		71235850	B2RCB5|Q86UE0|Q96M17	Missense_Mutation	SNP	ENST00000273936.5	37	CCDS3539.1	.	.	.	.	.	.	.	.	.	.	A	8.414	0.844917	0.16963	.	.	ENSG00000145309	ENST00000273936	T	0.28255	1.62	4.72	2.19	0.27852	.	0.272907	0.26601	N	0.023478	T	0.14184	0.0343	N	0.14661	0.345	0.09310	N	1	B	0.16802	0.019	B	0.17433	0.018	T	0.15838	-1.0423	10	0.30078	T	0.28	-28.786	3.6126	0.08066	0.7008:0.0:0.1094:0.1898	.	169	Q96KC9	CABS1_HUMAN	G	169	ENSP00000273936:S169G	ENSP00000273936:S169G	S	+	1	0	CABS1	71235850	0.015000	0.18098	0.001000	0.08648	0.025000	0.11179	2.358000	0.44134	0.366000	0.24427	-0.333000	0.08304	AGC		0.443	CABS1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251561.3	NM_033122	
ANKRD17	26057	hgsc.bcm.edu	37	4	74019691	74019691	+	Silent	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:74019691C>T	ENST00000358602.4	-	6	1256	c.1140G>A	c.(1138-1140)gtG>gtA	p.V380V	ANKRD17_ENST00000514252.1_5'Flank|ANKRD17_ENST00000509867.2_Silent_p.V267V|ANKRD17_ENST00000330838.6_Silent_p.V380V	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	380					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TGGCTACTTCCACATGTCCAG	0.428																																																	0			4											139.0	129.0	133.0					4																	74019691		2203	4300	6503	74238555	SO:0001819	synonymous_variant	26057			AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"""Ankyrin repeat domain containing"""	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.1140G>A	4.37:g.74019691C>T			74238555	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Silent	SNP	ENST00000358602.4	37	CCDS34004.1																																																																																				0.428	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217	
SFRP2	6423	hgsc.bcm.edu	37	4	154702675	154702675	+	Silent	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:154702675C>T	ENST00000274063.4	-	3	1100	c.816G>A	c.(814-816)tcG>tcA	p.S272S		NM_003013.2	NP_003004.1	Q96HF1	SFRP2_HUMAN	secreted frizzled-related protein 2	272	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				bone morphogenesis (GO:0060349)|brain development (GO:0007420)|cardiac left ventricle morphogenesis (GO:0003214)|cell-cell signaling (GO:0007267)|cellular response to extracellular stimulus (GO:0031668)|cellular response to X-ray (GO:0071481)|chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|convergent extension involved in axis elongation (GO:0060028)|digestive tract morphogenesis (GO:0048546)|embryonic digit morphogenesis (GO:0042733)|gonad development (GO:0008406)|hematopoietic stem cell proliferation (GO:0071425)|male gonad development (GO:0008584)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dermatome development (GO:0061185)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of gene expression (GO:0010629)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of mesodermal cell fate specification (GO:0042662)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-anal tail morphogenesis (GO:0036342)|regulation of stem cell division (GO:2000035)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|sclerotome development (GO:0061056)|vasculature development (GO:0001944)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase activator activity (GO:0061133)|fibronectin binding (GO:0001968)|integrin binding (GO:0005178)|metalloenzyme activator activity (GO:0010577)|PDZ domain binding (GO:0030165)|receptor agonist activity (GO:0048018)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.S272S(1)		breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	16	all_hematologic(180;0.093)	Renal(120;0.117)				ACCGCTTCACCGAGGTGATCA	0.592																																																	1	Substitution - coding silent(1)	ovary(1)	4											133.0	101.0	111.0					4																	154702675		2203	4300	6503	154922125	SO:0001819	synonymous_variant	6423			AF017986	CCDS34082.1	4q31.3	2008-08-29			ENSG00000145423	ENSG00000145423		"""Secreted frizzled-related proteins"""	10777	protein-coding gene	gene with protein product		604157				9391078	Standard	NM_003013		Approved	SARP1, SDF-5, FRP-2	uc003inv.1	Q96HF1	OTTHUMG00000161559	ENST00000274063.4:c.816G>A	4.37:g.154702675C>T			154922125	B3KQR2|O14778|Q9HAP5	Silent	SNP	ENST00000274063.4	37	CCDS34082.1																																																																																				0.592	SFRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365296.1		
C2orf44	80304	hgsc.bcm.edu	37	2	24261804	24261804	+	Silent	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:24261804A>G	ENST00000295148.4	-	2	618	c.561T>C	c.(559-561)gcT>gcC	p.A187A	C2orf44_ENST00000406895.3_Silent_p.A187A	NM_025203.2	NP_079479.1	Q9H6R7	CB044_HUMAN	chromosome 2 open reading frame 44	187									C2orf44/ALK(2)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAGTCTTCTGAGCGCTGTCCC	0.557			T	ALK	NSCLC																																			Dom	yes		2	2p23.3	80304	chromosome 2 open reading frame 44		E	0			2											53.0	48.0	50.0					2																	24261804		2203	4300	6503	24115308	SO:0001819	synonymous_variant	80304			AK025598	CCDS1705.1, CCDS46229.1	2p23.3	2012-07-30			ENSG00000163026	ENSG00000163026			26157	protein-coding gene	gene with protein product						22327622	Standard	NM_025203		Approved	FLJ21945	uc002rep.2	Q9H6R7	OTTHUMG00000125498	ENST00000295148.4:c.561T>C	2.37:g.24261804A>G			24115308	D6W532|Q8IYK0|Q9HBP5	Silent	SNP	ENST00000295148.4	37	CCDS1705.1																																																																																				0.557	C2orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246825.1	NM_025203	
PLB1	151056	hgsc.bcm.edu	37	2	28851975	28851975	+	Silent	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:28851975C>T	ENST00000327757.5	+	53	3785	c.3741C>T	c.(3739-3741)ttC>ttT	p.F1247F	PLB1_ENST00000422425.2_Silent_p.F1236F|PLB1_ENST00000541605.1_Silent_p.F212F	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	1247	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					CAAGGGCTTTCGTCAACGTGG	0.597																																																	0			2											85.0	68.0	74.0					2																	28851975		2203	4300	6503	28705479	SO:0001819	synonymous_variant	151056				CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.3741C>T	2.37:g.28851975C>T			28705479	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Silent	SNP	ENST00000327757.5	37	CCDS33168.1	.	.	.	.	.	.	.	.	.	.	C	6.396	0.441236	0.12164	.	.	ENSG00000163803	ENST00000404858	.	.	.	5.75	-1.99	0.07457	.	.	.	.	.	T	0.34077	0.0885	.	.	.	0.22620	N	0.998929	.	.	.	.	.	.	T	0.33727	-0.9857	4	.	.	.	-25.1842	10.4716	0.44640	0.0:0.4002:0.0:0.5998	.	.	.	.	L	1235	.	.	S	+	2	0	PLB1	28705479	0.000000	0.05858	0.002000	0.10522	0.808000	0.45660	-0.824000	0.04438	-0.803000	0.04415	0.561000	0.74099	TCG		0.597	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		
BIRC6	57448	hgsc.bcm.edu	37	2	32654233	32654233	+	Silent	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:32654233C>T	ENST00000421745.2	+	11	3026	c.2892C>T	c.(2890-2892)ctC>ctT	p.L964L		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	964					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TTCATTTTCTCCAAATTGGAG	0.333																																					Pancreas(94;175 1509 16028 18060 45422)												0			2											67.0	64.0	65.0					2																	32654233		2202	4298	6500	32507737	SO:0001819	synonymous_variant	57448			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.2892C>T	2.37:g.32654233C>T			32507737	Q9ULD1	Silent	SNP	ENST00000421745.2	37	CCDS33175.2																																																																																				0.333	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
REL	5966	hgsc.bcm.edu	37	2	61144021	61144021	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:61144021A>G	ENST00000295025.8	+	5	724	c.404A>G	c.(403-405)aAa>aGa	p.K135R	REL_ENST00000394479.3_Missense_Mutation_p.K135R	NM_002908.2	NP_002899.1	Q04864	REL_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog	135	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				cytokine production (GO:0001816)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of neuron death (GO:1901215)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(3)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	16	all_hematologic(2;0.0797)	Ovarian(717;0.0728)	LUSC - Lung squamous cell carcinoma(5;6.2e-08)|Lung(5;1.65e-06)|Epithelial(17;0.064)|all cancers(80;0.221)			GTCCCTGAAAAACAGCTGAAT	0.373			A		Hodgkin Lymphoma																																			Dom	yes		2	2p13-p12	5966	v-rel reticuloendotheliosis viral oncogene homolog (avian)		L	0			2											135.0	126.0	129.0					2																	61144021		2203	4300	6503	60997525	SO:0001583	missense	5966			M11595	CCDS1864.1, CCDS74515.1	2p13-p12	2013-07-09	2013-07-09		ENSG00000162924	ENSG00000162924			9954	protein-coding gene	gene with protein product		164910				1577270	Standard	XM_005264470		Approved	I-Rel, c-Rel	uc002sam.1	Q04864	OTTHUMG00000129418	ENST00000295025.8:c.404A>G	2.37:g.61144021A>G	ENSP00000295025:p.Lys135Arg		60997525	Q17RU2|Q2PNZ7|Q6LDY0	Missense_Mutation	SNP	ENST00000295025.8	37	CCDS1864.1	.	.	.	.	.	.	.	.	.	.	A	14.96	2.691014	0.48097	.	.	ENSG00000162924	ENST00000295025;ENST00000394479	T;T	0.44881	0.91;0.91	5.82	1.98	0.26296	Rel homology (3);p53-like transcription factor, DNA-binding (1);	0.373499	0.28465	N	0.015245	T	0.26666	0.0652	N	0.13168	0.305	0.22531	N	0.999019	B;B	0.29481	0.007;0.245	B;B	0.31101	0.003;0.124	T	0.12167	-1.0558	10	0.33141	T	0.24	-19.9427	13.8012	0.63202	0.6049:0.3951:0.0:0.0	.	135;135	Q17RU2;Q04864	.;REL_HUMAN	R	135	ENSP00000295025:K135R;ENSP00000377989:K135R	ENSP00000295025:K135R	K	+	2	0	REL	60997525	1.000000	0.71417	0.978000	0.43139	0.996000	0.88848	3.333000	0.52090	0.066000	0.16515	0.482000	0.46254	AAA		0.373	REL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251576.3	NM_002908	
GKN1	56287	hgsc.bcm.edu	37	2	69206108	69206108	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:69206108A>G	ENST00000377938.2	+	4	415	c.352A>G	c.(352-354)Aag>Gag	p.K118E		NM_019617.3	NP_062563.3	Q9NS71	GKN1_HUMAN	gastrokine 1	118	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.		K -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		digestion (GO:0007586)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)	extracellular region (GO:0005576)|secretory granule (GO:0030141)				breast(2)|large_intestine(4)|lung(5)	11						GGTCAAGGAAAAGAAGGTAAA	0.398																																																	0			2											66.0	61.0	63.0					2																	69206108		2203	4300	6503	69059612	SO:0001583	missense	56287			AY139182	CCDS1891.2	2p13.3	2012-10-10			ENSG00000169605	ENSG00000169605		"""BRICHOS domain containing"""	23217	protein-coding gene	gene with protein product	"""BRICHOS domain containing 1"""	606402				12851218, 11562744	Standard	NM_019617		Approved	AMP18, CA11, BRICD1	uc002sfc.3	Q9NS71	OTTHUMG00000129574	ENST00000377938.2:c.352A>G	2.37:g.69206108A>G	ENSP00000367172:p.Lys118Glu		69059612	Q8IUA9	Missense_Mutation	SNP	ENST00000377938.2	37	CCDS1891.2	.	.	.	.	.	.	.	.	.	.	A	12.17	1.856858	0.32791	.	.	ENSG00000169605	ENST00000377938	T	0.79653	-1.29	5.55	1.7	0.24286	BRICHOS (2);	0.482216	0.22022	N	0.065703	T	0.79441	0.4446	M	0.68952	2.095	0.20307	N	0.999912	P	0.40144	0.704	B	0.42462	0.388	T	0.70741	-0.4789	10	0.56958	D	0.05	-3.6789	11.8499	0.52405	0.5661:0.4339:0.0:0.0	.	118	Q9NS71	GKN1_HUMAN	E	118	ENSP00000367172:K118E	ENSP00000367172:K118E	K	+	1	0	GKN1	69059612	0.999000	0.42202	0.361000	0.25849	0.564000	0.35744	1.836000	0.39191	0.144000	0.18951	0.529000	0.55759	AAG		0.398	GKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251769.2	NM_019617	
DQX1	165545	hgsc.bcm.edu	37	2	74746786	74746786	+	Missense_Mutation	SNP	T	T	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:74746786T>A	ENST00000404568.3	-	10	1922	c.1703A>T	c.(1702-1704)gAa>gTa	p.E568V	DQX1_ENST00000393951.2_Missense_Mutation_p.E568V	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1	568						nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						TTGCATGAGTTCTAGGAGTTC	0.517																																																	0			2											140.0	136.0	137.0					2																	74746786		2203	4300	6503	74600294	SO:0001583	missense	165545			AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"""DEAQ box polypeptide 1 (RNA-dependent ATPase)"""				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965	ENST00000404568.3:c.1703A>T	2.37:g.74746786T>A	ENSP00000384621:p.Glu568Val		74600294	Q6B017|Q8NAM8	Missense_Mutation	SNP	ENST00000404568.3	37	CCDS1949.2	.	.	.	.	.	.	.	.	.	.	T	22.6	4.312198	0.81358	.	.	ENSG00000144045	ENST00000393951;ENST00000404568	T;T	0.03272	3.99;3.99	5.6	4.37	0.52481	Domain of unknown function DUF1605 (1);	0.072484	0.52532	D	0.000064	T	0.12347	0.0300	M	0.62723	1.935	0.46874	D	0.999235	D	0.69078	0.997	D	0.65874	0.939	T	0.00775	-1.1571	10	0.45353	T	0.12	-15.8884	10.5168	0.44894	0.0:0.0:0.1624:0.8376	.	568	Q8TE96	DQX1_HUMAN	V	568	ENSP00000377523:E568V;ENSP00000384621:E568V	ENSP00000377523:E568V	E	-	2	0	DQX1	74600294	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.732000	0.68563	2.119000	0.64992	0.482000	0.46254	GAA		0.517	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637	
ANKRD23	200539	hgsc.bcm.edu	37	2	97507799	97507799	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:97507799T>C	ENST00000318357.4	-	3	339	c.298A>G	c.(298-300)Aag>Gag	p.K100E	ANKRD23_ENST00000418232.1_Missense_Mutation_p.K100E|ANKRD23_ENST00000476975.1_5'UTR|ANKRD23_ENST00000331001.2_Missense_Mutation_p.K100E	NM_144994.7	NP_659431.5	Q86SG2	ANR23_HUMAN	ankyrin repeat domain 23	100					fatty acid metabolic process (GO:0006631)|response to mechanical stimulus (GO:0009612)	I band (GO:0031674)|intercalated disc (GO:0014704)|nucleus (GO:0005634)	titin binding (GO:0031432)			endometrium(2)|kidney(1)|lung(4)|ovary(1)|prostate(1)	9						CCACTCACCTTAACCAGGGGC	0.567																																																	0			2											76.0	79.0	78.0					2																	97507799		2203	4300	6503	96871526	SO:0001583	missense	200539				CCDS2027.1	2q11.2	2013-01-10			ENSG00000163126	ENSG00000163126		"""Ankyrin repeat domain containing"""	24470	protein-coding gene	gene with protein product	"""diabetes related ankyrin repeat protein"""	610736				12456686	Standard	NM_144994		Approved	DARP, FLJ32449, MARP3	uc002sxa.3	Q86SG2	OTTHUMG00000130534	ENST00000318357.4:c.298A>G	2.37:g.97507799T>C	ENSP00000321679:p.Lys100Glu		96871526	Q711K7|Q8NAJ7	Missense_Mutation	SNP	ENST00000318357.4	37	CCDS2027.1	.	.	.	.	.	.	.	.	.	.	T	8.832	0.940081	0.18281	.	.	ENSG00000163126	ENST00000318357;ENST00000418232;ENST00000331001	T;T;T	0.66815	-0.23;-0.23;-0.11	4.49	0.711	0.18162	.	0.572709	0.14581	N	0.310849	T	0.31796	0.0808	N	0.03983	-0.305	0.53688	D	0.999979	B;B	0.28971	0.229;0.0	B;B	0.30572	0.117;0.002	T	0.35251	-0.9796	10	0.02654	T	1	-7.3166	3.2878	0.06937	0.0:0.3535:0.2619:0.3846	.	100;100	Q86SG2-2;Q86SG2	.;ANR23_HUMAN	E	100	ENSP00000321679:K100E;ENSP00000398987:K100E;ENSP00000333108:K100E	ENSP00000321679:K100E	K	-	1	0	ANKRD23	96871526	0.392000	0.25229	0.629000	0.29254	0.633000	0.38033	0.354000	0.20146	0.294000	0.22547	0.454000	0.30748	AAG		0.567	ANKRD23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252956.1	NM_144994	
VWA3B	200403	hgsc.bcm.edu	37	2	98804463	98804463	+	Missense_Mutation	SNP	C	C	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:98804463C>A	ENST00000477737.1	+	10	1541	c.1337C>A	c.(1336-1338)gCa>gAa	p.A446E	VWA3B_ENST00000435344.1_Missense_Mutation_p.A446E|VWA3B_ENST00000451075.2_Missense_Mutation_p.A296E	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	446										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						ACAGTCCATGCAAAATATTGC	0.478																																																	0			2											82.0	80.0	81.0					2																	98804463		1935	4148	6083	98170895	SO:0001583	missense	200403			AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.1337C>A	2.37:g.98804463C>A	ENSP00000417955:p.Ala446Glu		98170895	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.240018	0.79912	.	.	ENSG00000168658	ENST00000435344;ENST00000477737;ENST00000451075	T;T;T	0.27890	1.64;3.02;2.37	4.76	4.76	0.60689	.	0.000000	0.56097	D	0.000035	T	0.49881	0.1583	L	0.47716	1.5	0.31642	N	0.647958	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	T	0.57219	-0.7849	10	0.72032	D	0.01	.	16.8999	0.86110	0.0:1.0:0.0:0.0	.	296;446;446	B7Z7Q7;Q502W6;Q502W6-8	.;VWA3B_HUMAN;.	E	446;446;296	ENSP00000401959:A446E;ENSP00000417955:A446E;ENSP00000389463:A296E	ENSP00000388158:A446E	A	+	2	0	VWA3B	98170895	0.999000	0.42202	1.000000	0.80357	0.947000	0.59692	5.259000	0.65485	2.336000	0.79503	0.460000	0.39030	GCA		0.478	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	
IL1RL1	9173	hgsc.bcm.edu	37	2	102959786	102959786	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:102959786A>G	ENST00000233954.1	+	8	1152	c.881A>G	c.(880-882)gAa>gGa	p.E294G	IL1RL1_ENST00000404917.2_Missense_Mutation_p.E177G|IL1RL1_ENST00000311734.2_Missense_Mutation_p.E294G|IL1RL1_ENST00000409584.1_Missense_Mutation_p.E280G	NM_016232.4	NP_057316.3	Q01638	ILRL1_HUMAN	interleukin 1 receptor-like 1	294	Ig-like C2-type 3.				immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of macrophage activation (GO:0043032)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|interleukin-1 receptor activity (GO:0004908)|interleukin-33 receptor activity (GO:0002114)|receptor signaling protein activity (GO:0005057)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(3)|urinary_tract(1)	16						GACGTGAAGGAAGAGGATTTA	0.438																																																	0			2											210.0	193.0	199.0					2																	102959786		2203	4300	6503	102326218	SO:0001583	missense	9173			D12764	CCDS2057.1, CCDS2058.1, CCDS74548.1	2q12	2013-01-29			ENSG00000115602	ENSG00000115602		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5998	protein-coding gene	gene with protein product	"""homolog of mouse growth stimulation-expressed"""	601203				1482686, 10191101, 16286016	Standard	NM_016232		Approved	ST2, FIT-1, ST2L, ST2V, DER4, T1, IL33R	uc002tbu.1	Q01638	OTTHUMG00000130782	ENST00000233954.1:c.881A>G	2.37:g.102959786A>G	ENSP00000233954:p.Glu294Gly		102326218	A8K6B3|B4E0I3|Q53TU7|Q8NEJ3|Q9ULV7|Q9UQ44	Missense_Mutation	SNP	ENST00000233954.1	37	CCDS2057.1	.	.	.	.	.	.	.	.	.	.	A	11.70	1.717141	0.30413	.	.	ENSG00000115602	ENST00000233954;ENST00000404917;ENST00000311734;ENST00000409584	T;T;T;T	0.14516	4.02;4.02;4.02;2.5	5.19	5.19	0.71726	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.630980	0.16451	N	0.213845	T	0.25606	0.0623	M	0.75447	2.3	0.58432	D	0.999996	D;D;P	0.55172	0.97;0.962;0.858	P;B;B	0.49853	0.624;0.441;0.345	T	0.01516	-1.1335	10	0.49607	T	0.09	.	11.3494	0.49579	1.0:0.0:0.0:0.0	.	177;294;294	B4E0I3;Q01638-2;Q01638	.;.;ILRL1_HUMAN	G	294;177;294;280	ENSP00000233954:E294G;ENSP00000384822:E177G;ENSP00000310371:E294G;ENSP00000386618:E280G	ENSP00000233954:E294G	E	+	2	0	IL1RL1	102326218	0.821000	0.29204	0.152000	0.22495	0.075000	0.17131	2.936000	0.48971	2.180000	0.69256	0.477000	0.44152	GAA		0.438	IL1RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253296.1	NM_016232	
CCNT2	905	hgsc.bcm.edu	37	2	135711084	135711084	+	Silent	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:135711084A>G	ENST00000264157.5	+	9	1089	c.1059A>G	c.(1057-1059)caA>caG	p.Q353Q	CCNT2_ENST00000537343.1_Silent_p.Q178Q|CCNT2_ENST00000295238.6_Silent_p.Q353Q	NM_001241.3|NM_058241.2	NP_001232.1|NP_490595.1	O60583	CCNT2_HUMAN	cyclin T2	353					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(2)|kidney(3)|large_intestine(10)|lung(6)|ovary(2)|prostate(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.107)		aatggcctcaacaTCAAGACT	0.428																																																	0			2											109.0	99.0	102.0					2																	135711084		2203	4300	6503	135427554	SO:0001819	synonymous_variant	905			AF048731	CCDS2174.1, CCDS2175.1	2q21.3	2010-11-15			ENSG00000082258	ENSG00000082258			1600	protein-coding gene	gene with protein product		603862				9499409, 10465067	Standard	NM_001241		Approved		uc002tuc.2	O60583	OTTHUMG00000131712	ENST00000264157.5:c.1059A>G	2.37:g.135711084A>G			135427554	A8KA48|D3DP73|D3DP74|O60582|Q29R66|Q53SR4|Q5I1Y0	Silent	SNP	ENST00000264157.5	37	CCDS2174.1																																																																																				0.428	CCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254629.1	NM_058241	
PPIG	9360	hgsc.bcm.edu	37	2	170493347	170493347	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:170493347A>G	ENST00000260970.3	+	14	1799	c.1579A>G	c.(1579-1581)Agt>Ggt	p.S527G	PPIG_ENST00000448752.2_Missense_Mutation_p.S527G|PPIG_ENST00000409714.3_Missense_Mutation_p.S512G	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	527					protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)	p.S527G(1)		NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	AGAATCAAAGAGTAATGAGCA	0.333																																																	1	Substitution - Missense(1)	ovary(1)	2											55.0	54.0	54.0					2																	170493347		2203	4300	6503	170201593	SO:0001583	missense	9360			X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"""SR-related CTD-associated factor 10"""	606093	"""peptidyl-prolyl isomerase G (cyclophilin G)"""			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.1579A>G	2.37:g.170493347A>G	ENSP00000260970:p.Ser527Gly		170201593	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Missense_Mutation	SNP	ENST00000260970.3	37	CCDS2235.1	.	.	.	.	.	.	.	.	.	.	A	12.96	2.094862	0.36952	.	.	ENSG00000138398	ENST00000260970;ENST00000409714;ENST00000448752	T;T;T	0.18338	2.22;2.22;2.22	5.74	5.74	0.90152	.	0.211109	0.49305	D	0.000152	T	0.11110	0.0271	N	0.19112	0.55	0.35355	D	0.787679	B;P;B	0.39782	0.043;0.688;0.043	B;B;B	0.28849	0.027;0.095;0.027	T	0.17228	-1.0376	10	0.49607	T	0.09	-14.9731	16.0351	0.80621	1.0:0.0:0.0:0.0	.	512;512;527	E9PG73;Q2NKQ6;Q13427	.;.;PPIG_HUMAN	G	527;512;527	ENSP00000260970:S527G;ENSP00000386245:S512G;ENSP00000407083:S527G	ENSP00000260970:S527G	S	+	1	0	PPIG	170201593	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.777000	0.55364	2.186000	0.69663	0.533000	0.62120	AGT		0.333	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2		
PPIG	9360	hgsc.bcm.edu	37	2	170493409	170493409	+	Silent	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:170493409A>G	ENST00000260970.3	+	14	1861	c.1641A>G	c.(1639-1641)agA>agG	p.R547R	PPIG_ENST00000448752.2_Silent_p.R547R|PPIG_ENST00000409714.3_Silent_p.R532R	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	547	Arg/Ser-rich (RS domain).				protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)	p.R547R(1)		NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	CCAGGAGTAGAGAATGTGATA	0.388																																																	1	Substitution - coding silent(1)	ovary(1)	2											84.0	81.0	82.0					2																	170493409		2203	4300	6503	170201655	SO:0001819	synonymous_variant	9360			X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"""SR-related CTD-associated factor 10"""	606093	"""peptidyl-prolyl isomerase G (cyclophilin G)"""			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.1641A>G	2.37:g.170493409A>G			170201655	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Silent	SNP	ENST00000260970.3	37	CCDS2235.1																																																																																				0.388	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2		
MYO3B	140469	hgsc.bcm.edu	37	2	171056662	171056662	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:171056662T>C	ENST00000408978.4	+	3	332	c.189T>C	c.(187-189)gaT>gaC	p.D63D	MYO3B_ENST00000409044.3_Silent_p.D63D|MYO3B_ENST00000334231.6_Silent_p.D72D|MYO3B_ENST00000602629.1_3'UTR	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	63	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						CTGTTTAGGATATGGATGAAG	0.353																																																	0			2											91.0	89.0	90.0					2																	171056662		1856	4112	5968	170764908	SO:0001819	synonymous_variant	140469				CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"""Myosins / Myosin superfamily : Class III"""	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.189T>C	2.37:g.171056662T>C			170764908	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	37	CCDS42773.1	.	.	.	.	.	.	.	.	.	.	T	12.99	2.103198	0.37145	.	.	ENSG00000071909	ENST00000442690	.	.	.	5.52	0.219	0.15274	.	.	.	.	.	T	0.56848	0.2013	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49485	-0.8935	4	.	.	.	.	9.4898	0.38953	0.0:0.288:0.0:0.712	.	.	.	.	H	63	.	.	Y	+	1	0	MYO3B	170764908	1.000000	0.71417	0.997000	0.53966	0.967000	0.64934	0.805000	0.27112	-0.125000	0.11703	-0.274000	0.10170	TAT		0.353	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
CIR1	9541	hgsc.bcm.edu	37	2	175213553	175213553	+	Missense_Mutation	SNP	T	T	C	rs200766128		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:175213553T>C	ENST00000342016.3	-	10	1117	c.1025A>G	c.(1024-1026)gAg>gGg	p.E342G	CIR1_ENST00000362053.5_3'UTR	NM_004882.3	NP_004873.3	Q86X95	CIR1_HUMAN	corepressor interacting with RBPJ, 1	342	Lys/Ser-rich.				mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.E342G(1)		central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(5)|skin(1)	15						CCTAGAACTCTCGTGTTTTAA	0.443																																																	1	Substitution - Missense(1)	central_nervous_system(1)	2											159.0	159.0	159.0					2																	175213553		2203	4300	6503	174921799	SO:0001583	missense	7335			AF098297	CCDS2256.1	2q31.1	2009-07-14			ENSG00000138433	ENSG00000138433			24217	protein-coding gene	gene with protein product	"""recepin"", ""CBF1 interacting corepressor"""	605228				15652350, 11222720, 9874765	Standard	NM_004882		Approved	CIR	uc002uim.3	Q86X95	OTTHUMG00000132338	ENST00000342016.3:c.1025A>G	2.37:g.175213553T>C	ENSP00000339723:p.Glu342Gly		174921799	A6NFI6|A8K8M4|O95367|Q12804|Q4G1B9|Q6PJI4|Q8IWI2	Missense_Mutation	SNP	ENST00000342016.3	37	CCDS2256.1	.	.	.	.	.	.	.	.	.	.	T	9.932	1.215039	0.22373	.	.	ENSG00000138433	ENST00000342016	.	.	.	6.16	5.01	0.66863	.	0.277370	0.34531	N	0.003885	T	0.53384	0.1793	L	0.56769	1.78	0.34740	D	0.730643	B;B	0.17465	0.022;0.012	B;B	0.17433	0.018;0.005	T	0.61173	-0.7116	9	0.59425	D	0.04	.	10.7341	0.46115	0.0:0.0721:0.0:0.9279	.	342;342	A0PJI7;Q86X95	.;CIR1_HUMAN	G	342	.	ENSP00000339723:E342G	E	-	2	0	CIR1	174921799	1.000000	0.71417	0.425000	0.26659	0.026000	0.11368	2.277000	0.43417	1.152000	0.42452	0.528000	0.53228	GAG		0.443	CIR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255460.1	NM_004882	
PLEKHA3	65977	hgsc.bcm.edu	37	2	179350384	179350384	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:179350384G>A	ENST00000234453.5	+	2	459	c.57G>A	c.(55-57)tgG>tgA	p.W19*	PLEKHA3_ENST00000461474.1_3'UTR	NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3	19	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			AGCCTCGTTGGTTTGTTTTAG	0.358																																																	0			2											114.0	113.0	113.0					2																	179350384		2203	4300	6503	179058630	SO:0001587	stop_gained	65977			AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"""Pleckstrin homology (PH) domain containing"""	14338	protein-coding gene	gene with protein product	"""four-phosphate-adaptor protein 1"""	607774	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"""			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446	ENST00000234453.5:c.57G>A	2.37:g.179350384G>A	ENSP00000234453:p.Trp19*		179058630	Q4ZG69|Q86TQ1|Q9NXT3	Nonsense_Mutation	SNP	ENST00000234453.5	37	CCDS33336.1	.	.	.	.	.	.	.	.	.	.	G	35	5.502460	0.96371	.	.	ENSG00000116095	ENST00000234453	.	.	.	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.3514	18.6285	0.91350	0.0:0.0:1.0:0.0	.	.	.	.	X	19	.	ENSP00000234453:W19X	W	+	3	0	PLEKHA3	179058630	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.864000	0.99589	2.380000	0.81148	0.563000	0.77884	TGG		0.358	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2	NM_019091	
AOX1	316	hgsc.bcm.edu	37	2	201527647	201527647	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:201527647T>C	ENST00000374700.2	+	31	3739	c.3498T>C	c.(3496-3498)gcT>gcC	p.A1166A	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	1166					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	TTTATGGAGCTGCCTGTTCCG	0.468																																																	0			2											160.0	150.0	153.0					2																	201527647		2203	4300	6503	201235892	SO:0001819	synonymous_variant	316			AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.3498T>C	2.37:g.201527647T>C			201235892	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Silent	SNP	ENST00000374700.2	37	CCDS33360.1																																																																																				0.468	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159	
RAPH1	65059	hgsc.bcm.edu	37	2	204354499	204354499	+	Missense_Mutation	SNP	T	T	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:204354499T>A	ENST00000319170.5	-	4	839	c.540A>T	c.(538-540)aaA>aaT	p.K180N	RAPH1_ENST00000439222.1_Missense_Mutation_p.K180N|RAPH1_ENST00000308091.4_Missense_Mutation_p.K180N|RAPH1_ENST00000419464.1_Missense_Mutation_p.K180N|RAPH1_ENST00000374493.3_Missense_Mutation_p.K180N|RAPH1_ENST00000374488.2_Missense_Mutation_p.K180N|RAPH1_ENST00000374489.2_Missense_Mutation_p.K180N|RAPH1_ENST00000418114.1_Missense_Mutation_p.K180N|RAPH1_ENST00000453034.1_Missense_Mutation_p.K180N|RAPH1_ENST00000457812.1_Missense_Mutation_p.K180N|RAPH1_ENST00000423104.1_Missense_Mutation_p.K180N	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	180					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TTACTAAGGGTTTAGTATCTT	0.473																																																	0			2											128.0	119.0	122.0					2																	204354499		2203	4300	6503	204062744	SO:0001583	missense	65059			AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"""Pleckstrin homology (PH) domain containing"""	14436	protein-coding gene	gene with protein product	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"""	609035	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"""	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.540A>T	2.37:g.204354499T>A	ENSP00000316543:p.Lys180Asn		204062744	Q96Q37|Q9C0I2	Missense_Mutation	SNP	ENST00000319170.5	37	CCDS2359.1	.	.	.	.	.	.	.	.	.	.	T	8.544	0.874019	0.17395	.	.	ENSG00000173166	ENST00000457812;ENST00000319170;ENST00000374493;ENST00000374489;ENST00000374488;ENST00000308091;ENST00000439222;ENST00000419464;ENST00000423104;ENST00000453034;ENST00000432342;ENST00000418114;ENST00000413201	T;T;T;T;T;T;T;T;T;T;T	0.48201	0.87;0.86;0.84;0.86;0.87;0.83;0.87;0.87;0.86;0.82;0.87	5.33	0.726	0.18248	.	0.000000	0.45606	D	0.000359	T	0.44052	0.1275	L	0.34521	1.04	0.39761	D	0.97202	P;P;D	0.60575	0.646;0.948;0.988	B;B;P	0.57204	0.173;0.431;0.815	T	0.27365	-1.0076	10	0.23302	T	0.38	-17.4432	8.4847	0.33065	0.0:0.4304:0.0:0.5696	.	180;180;180	Q70E73-6;C9K0J5;Q70E73	.;.;RAPH1_HUMAN	N	180	ENSP00000392854:K180N;ENSP00000316543:K180N;ENSP00000363617:K180N;ENSP00000363613:K180N;ENSP00000363612:K180N;ENSP00000311293:K180N;ENSP00000411138:K180N;ENSP00000390578:K180N;ENSP00000397751:K180N;ENSP00000406662:K180N;ENSP00000396711:K180N	ENSP00000311293:K180N	K	-	3	2	RAPH1	204062744	0.988000	0.35896	0.578000	0.28575	0.164000	0.22412	0.065000	0.14466	0.233000	0.21120	-0.973000	0.02599	AAA		0.473	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252	
PIKFYVE	200576	hgsc.bcm.edu	37	2	209190290	209190290	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:209190290C>T	ENST00000264380.4	+	20	2913	c.2755C>T	c.(2755-2757)Cct>Tct	p.P919S		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	919					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						TGACATCCCTCCTGAGTCTCT	0.522																																																	0			2											74.0	68.0	70.0					2																	209190290		2203	4300	6503	208898535	SO:0001583	missense	200576			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"""Zinc fingers, FYVE domain containing"""	23785	protein-coding gene	gene with protein product	"""zinc finger, FYVE domain containing 29"""	609414	"""phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"""	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.2755C>T	2.37:g.209190290C>T	ENSP00000264380:p.Pro919Ser		208898535	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.556806	0.00138	.	.	ENSG00000115020	ENST00000264380;ENST00000392200;ENST00000452564	T;T	0.26373	1.74;1.9	6.07	2.19	0.27852	.	0.716341	0.13266	N	0.400875	T	0.08935	0.0221	N	0.04043	-0.29	0.26934	N	0.966409	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.37865	-0.9687	10	0.05721	T	0.95	-0.6125	6.2846	0.21027	0.0:0.6143:0.1232:0.2624	.	919;863	Q9Y2I7;E9PDH4	FYV1_HUMAN;.	S	919;495;863	ENSP00000264380:P919S;ENSP00000405736:P863S	ENSP00000264380:P919S	P	+	1	0	PIKFYVE	208898535	0.000000	0.05858	0.004000	0.12327	0.120000	0.20174	-0.051000	0.11885	0.407000	0.25591	-0.143000	0.13931	CCT		0.522	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
SPAG16	79582	hgsc.bcm.edu	37	2	214228834	214228834	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:214228834A>G	ENST00000331683.5	+	8	892	c.797A>G	c.(796-798)cAa>cGa	p.Q266R	SPAG16_ENST00000414961.2_3'UTR|SPAG16_ENST00000272898.7_Missense_Mutation_p.Q266R|SPAG16_ENST00000413312.1_Missense_Mutation_p.Q235R|SPAG16_ENST00000447990.1_Missense_Mutation_p.Q266R|SPAG16_ENST00000374309.3_Missense_Mutation_p.Q172R	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	266					cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		AAGAAACTGCAAAGAGGACAT	0.289																																																	0			2											28.0	28.0	28.0					2																	214228834		2201	4273	6474	213937079	SO:0001583	missense	79582			AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"""WD repeat domain containing"""	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.797A>G	2.37:g.214228834A>G	ENSP00000332592:p.Gln266Arg		213937079	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	.	.	.	.	.	.	.	.	.	.	A	11.60	1.687834	0.29962	.	.	ENSG00000144451	ENST00000331683;ENST00000413312;ENST00000272898;ENST00000447990;ENST00000374309	T;T	0.57273	0.5;0.41	4.83	4.83	0.62350	.	0.418505	0.24452	N	0.038420	T	0.34483	0.0899	N	0.12182	0.205	0.09310	N	1	B;B;B;B;B	0.19200	0.009;0.017;0.034;0.009;0.0	B;B;B;B;B	0.15870	0.007;0.011;0.014;0.003;0.0	T	0.32375	-0.9909	10	0.72032	D	0.01	.	11.0856	0.48084	1.0:0.0:0.0:0.0	.	172;117;235;206;266	B4DYB5;Q8N0X2-2;Q8N0X2-3;Q4G1A2;Q8N0X2	.;.;.;.;SPG16_HUMAN	R	266;235;266;266;172	ENSP00000332592:Q266R;ENSP00000363428:Q172R	ENSP00000272898:Q266R	Q	+	2	0	SPAG16	213937079	0.884000	0.30299	0.086000	0.20670	0.002000	0.02628	2.666000	0.46799	1.940000	0.56252	0.528000	0.53228	CAA		0.289	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532	
TNS1	7145	hgsc.bcm.edu	37	2	218713758	218713758	+	Silent	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:218713758C>T	ENST00000171887.4	-	17	1559	c.1107G>A	c.(1105-1107)gtG>gtA	p.V369V	TNS1_ENST00000480665.1_5'UTR|TNS1_ENST00000430930.1_Silent_p.V369V|TNS1_ENST00000419504.1_Silent_p.V369V	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	369					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		CTTTCTTCTTCACCTTAGCAT	0.582																																																	0			2											139.0	134.0	136.0					2																	218713758		2203	4300	6503	218422003	SO:0001819	synonymous_variant	7145			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.1107G>A	2.37:g.218713758C>T			218422003	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																				0.582	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
AGFG1	3267	hgsc.bcm.edu	37	2	228418450	228418450	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:228418450A>G	ENST00000310078.8	+	12	1828	c.1568A>G	c.(1567-1569)aAg>aGg	p.K523R	AGFG1_ENST00000373671.3_Missense_Mutation_p.K483R|AGFG1_ENST00000409171.1_Missense_Mutation_p.K521R|AGFG1_ENST00000409315.1_Missense_Mutation_p.K502R|AGFG1_ENST00000409979.2_Missense_Mutation_p.K545R	NM_001135188.1|NM_001135189.1|NM_004504.4	NP_001128660.1|NP_001128661.1|NP_004495.2	P52594	AGFG1_HUMAN	ArfGAP with FG repeats 1	523					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of ARF GTPase activity (GO:0032312)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)	ARF GTPase activator activity (GO:0008060)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.K523R(1)|p.T522fs*3(1)		central_nervous_system(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(2)|ovary(1)|prostate(1)|skin(4)|stomach(1)	18						GGACAAACAAAGCCAGTAGTA	0.348																																																	2	Substitution - Missense(1)|Deletion - Frameshift(1)	ovary(1)|central_nervous_system(1)	2											102.0	109.0	107.0					2																	228418450		2203	4300	6503	228126694	SO:0001583	missense	3267				CCDS2467.1, CCDS46533.1, CCDS46534.1, CCDS46535.1	2q36	2009-11-30	2008-09-22	2008-09-22	ENSG00000173744	ENSG00000173744		"""ADP-ribosylation factor GTPase activating proteins"""	5175	protein-coding gene	gene with protein product		600862	"""HIV-1 Rev binding protein"""	HRB		7637788	Standard	NM_004504		Approved	RIP, RAB	uc002vpd.2	P52594	OTTHUMG00000133186	ENST00000310078.8:c.1568A>G	2.37:g.228418450A>G	ENSP00000312059:p.Lys523Arg		228126694	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Missense_Mutation	SNP	ENST00000310078.8	37	CCDS2467.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.2|24.2	4.500134|4.500134	0.85176|0.85176	.|.	.|.	ENSG00000173744|ENSG00000173744	ENST00000409979;ENST00000542592;ENST00000310078;ENST00000409315;ENST00000373671;ENST00000409171|ENST00000458212	T;T;T;T;T|.	0.32272|.	1.6;1.61;1.46;1.66;1.66|.	5.75|5.75	4.58|4.58	0.56647|0.56647	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.69088|0.69088	0.3072|0.3072	M|M	0.62723|0.62723	1.935|1.935	0.46356|0.46356	D|D	0.999|0.999	D;B;D;D|.	0.76494|.	0.998;0.392;0.997;0.999|.	D;B;D;P|.	0.80764|.	0.994;0.124;0.98;0.874|.	T|T	0.66925|0.66925	-0.5800|-0.5800	10|5	0.26408|.	T|.	0.33|.	.|.	13.0852|13.0852	0.59135|0.59135	0.8659:0.1341:0.0:0.0|0.8659:0.1341:0.0:0.0	.|.	483;521;545;523|.	P52594-2;P52594-3;E9PHX7;P52594|.	.;.;.;AGFG1_HUMAN|.	R|G	545;530;523;502;483;521|93	ENSP00000387282:K545R;ENSP00000312059:K523R;ENSP00000387154:K502R;ENSP00000362775:K483R;ENSP00000387218:K521R|.	ENSP00000312059:K523R|.	K|S	+|+	2|1	0|0	AGFG1|AGFG1	228126694|228126694	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.641000|6.641000	0.74324|0.74324	0.983000|0.983000	0.38602|0.38602	0.482000|0.482000	0.46254|0.46254	AAG|AGC		0.348	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504	
TRPM8	79054	hgsc.bcm.edu	37	2	234869684	234869684	+	Missense_Mutation	SNP	C	C	T	rs200707338		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:234869684C>T	ENST00000324695.4	+	12	1667	c.1627C>T	c.(1627-1629)Cgg>Tgg	p.R543W	TRPM8_ENST00000433712.2_Missense_Mutation_p.R231W	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	543					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	CAGAAATGGCCGGGACGAGAT	0.488																																																	0			2											61.0	56.0	57.0					2																	234869684		2203	4300	6503	234534423	SO:0001583	missense	79054			AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.1627C>T	2.37:g.234869684C>T	ENSP00000323926:p.Arg543Trp		234534423	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	37	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	C	13.42	2.231806	0.39399	.	.	ENSG00000144481	ENST00000324695;ENST00000433712	T;T	0.64438	-0.1;-0.1	5.65	3.26	0.37387	.	0.255433	0.35262	N	0.003332	T	0.51176	0.1659	N	0.19112	0.55	0.35794	D	0.822651	D;D	0.56968	0.975;0.978	P;P	0.46758	0.526;0.518	T	0.62397	-0.6863	10	0.72032	D	0.01	-32.9589	11.976	0.53091	0.5493:0.4507:0.0:0.0	.	231;543	A0AVG2;Q7Z2W7	.;TRPM8_HUMAN	W	543;231	ENSP00000323926:R543W;ENSP00000404423:R231W	ENSP00000323926:R543W	R	+	1	2	TRPM8	234534423	1.000000	0.71417	1.000000	0.80357	0.135000	0.20990	1.329000	0.33770	0.412000	0.25729	-0.262000	0.10625	CGG		0.488	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080	
ACKR3	57007	hgsc.bcm.edu	37	2	237489860	237489860	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:237489860G>A	ENST00000272928.3	+	2	1062	c.752G>A	c.(751-753)cGg>cAg	p.R251Q		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	251					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|receptor internalization (GO:0031623)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|scavenger receptor activity (GO:0005044)										CACAGCAGCCGGAAGATCATC	0.572																																																	0			2											123.0	103.0	110.0					2																	237489860		2203	4300	6503	237154599	SO:0001583	missense	57007			BC008459	CCDS2516.1	2q37.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144476	ENSG00000144476		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : Atypical"""	23692	protein-coding gene	gene with protein product		610376	"""chemokine orphan receptor 1"", ""chemokine (C-X-C motif) receptor 7"""	CMKOR1, CXCR7		16107333, 16148	Standard	NM_020311		Approved	RDC1, GPR159	uc002vwd.3	P25106	OTTHUMG00000133295	ENST00000272928.3:c.752G>A	2.37:g.237489860G>A	ENSP00000272928:p.Arg251Gln		237154599	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Missense_Mutation	SNP	ENST00000272928.3	37	CCDS2516.1	.	.	.	.	.	.	.	.	.	.	G	13.52	2.262677	0.39995	.	.	ENSG00000144476	ENST00000272928	T	0.71817	-0.6	5.8	3.69	0.42338	GPCR, rhodopsin-like superfamily (1);	0.121195	0.56097	D	0.000028	T	0.65059	0.2655	M	0.62723	1.935	0.41896	D	0.990391	B	0.27316	0.175	B	0.21151	0.033	T	0.63611	-0.6598	9	.	.	.	.	13.3954	0.60849	0.1478:0.0:0.8522:0.0	.	251	P25106	CXCR7_HUMAN	Q	251	ENSP00000272928:R251Q	.	R	+	2	0	CXCR7	237154599	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.686000	0.84128	1.457000	0.47850	0.655000	0.94253	CGG		0.572	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311	
COL6A3	1293	hgsc.bcm.edu	37	2	238277613	238277613	+	Missense_Mutation	SNP	G	G	A	rs146629310		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:238277613G>A	ENST00000295550.4	-	10	4945	c.4493C>T	c.(4492-4494)cCg>cTg	p.P1498L	COL6A3_ENST00000472056.1_Missense_Mutation_p.P891L|COL6A3_ENST00000409809.1_Missense_Mutation_p.P1292L|COL6A3_ENST00000353578.4_Missense_Mutation_p.P1292L|COL6A3_ENST00000346358.4_Missense_Mutation_p.P1298L|COL6A3_ENST00000347401.3_Missense_Mutation_p.P1297L	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1498	Nonhelical region.|VWFA 8. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		GTCCAGCACCGGGGCCTGGGA	0.537																																																	0			2						G	LEU/PRO,LEU/PRO,LEU/PRO	0,4406		0,0,2203	50.0	51.0	51.0		3875,2672,4493	1.1	0.0	2	dbSNP_134	51	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	COL6A3	NM_057167.3,NM_057166.4,NM_004369.3	98,98,98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	1292/2972,891/2571,1498/3178	238277613	1,13005	2203	4300	6503	237942352	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.4493C>T	2.37:g.238277613G>A	ENSP00000295550:p.Pro1498Leu		237942352	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	G	5.325	0.245290	0.10077	0.0	1.16E-4	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62;-1.62;-1.62	5.36	1.13	0.20643	von Willebrand factor, type A (3);	1.137570	0.06774	N	0.784062	T	0.69052	0.3068	N	0.11064	0.09	0.09310	N	1	B;B;B	0.25441	0.093;0.039;0.126	B;B;B	0.22753	0.032;0.01;0.041	T	0.55786	-0.8086	10	0.40728	T	0.16	.	10.5123	0.44868	0.0:0.2462:0.5122:0.2416	.	891;1292;1498	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	L	1498;1297;1292;891;1292;1298	ENSP00000295550:P1498L;ENSP00000315609:P1297L;ENSP00000315873:P1292L;ENSP00000418285:P891L;ENSP00000386844:P1292L;ENSP00000295546:P1298L	ENSP00000295550:P1498L	P	-	2	0	COL6A3	237942352	0.000000	0.05858	0.000000	0.03702	0.299000	0.27559	0.797000	0.26999	0.195000	0.20347	0.655000	0.94253	CCG		0.537	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
MLLT3	4300	hgsc.bcm.edu	37	9	20414187	20414187	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:20414187T>C	ENST00000380338.4	-	5	943	c.657A>G	c.(655-657)aaA>aaG	p.K219K	MLLT3_ENST00000475957.1_5'UTR|MIR4473_ENST00000583731.1_RNA|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.K216K	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	219					anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		TGGAAGGTTCTTTGAAGGCAC	0.388			T	MLL	ALL																																			Dom	yes		9	9p22	4300	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""		L	0			9											256.0	272.0	267.0					9																	20414187		2203	4300	6503	20404187	SO:0001819	synonymous_variant	4300			L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.657A>G	9.37:g.20414187T>C			20404187	B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	CCDS6494.1																																																																																				0.388	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529	
MLLT3	4300	hgsc.bcm.edu	37	9	20414343	20414343	+	Silent	SNP	A	A	G	rs372894655	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:20414343A>G	ENST00000380338.4	-	5	787	c.501T>C	c.(499-501)agT>agC	p.S167S	MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S164S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	167	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.S167S(19)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctgctactgctgctgc	0.532			T	MLL	ALL								A|||	612	0.122204	0.1505	0.1066	5008	,	,		12422	0.0833		0.0716	False		,,,				2504	0.1871							Dom	yes		9	9p22	4300	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""		L	19	Substitution - coding silent(19)	lung(8)|kidney(5)|endometrium(3)|central_nervous_system(1)|urinary_tract(1)|prostate(1)	9											8.0	15.0	13.0					9																	20414343		1537	3257	4794	20404343	SO:0001819	synonymous_variant	4300			L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.501T>C	9.37:g.20414343A>G			20404343	B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	CCDS6494.1																																																																																				0.532	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529	
VPS13A	23230	hgsc.bcm.edu	37	9	79966342	79966342	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:79966342G>A	ENST00000360280.3	+	53	7659	c.7399G>A	c.(7399-7401)Ggt>Agt	p.G2467S	VPS13A_ENST00000357409.5_Missense_Mutation_p.G2467S|VPS13A_ENST00000376634.4_Missense_Mutation_p.G2467S|VPS13A_ENST00000376636.3_Missense_Mutation_p.G2428S	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2467					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						AAAAAGCCATGGTGAAGTAAC	0.473																																																	0			9											164.0	159.0	161.0					9																	79966342		2203	4300	6503	79156162	SO:0001583	missense	23230			AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.7399G>A	9.37:g.79966342G>A	ENSP00000353422:p.Gly2467Ser		79156162	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.938545	0.73557	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.46819	1.03;0.86;0.94;1.03	5.19	5.19	0.71726	.	0.061993	0.64402	D	0.000005	T	0.63674	0.2531	M	0.72894	2.215	0.80722	D	1	P;D;D;D	0.71674	0.753;0.997;0.998;0.998	P;P;D;D	0.62955	0.511;0.908;0.909;0.909	T	0.58691	-0.7592	10	0.10377	T	0.69	.	18.6648	0.91485	0.0:0.0:1.0:0.0	.	2428;2467;2467;2467	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	S	2467;2428;2467;2467	ENSP00000365821:G2467S;ENSP00000365823:G2428S;ENSP00000353422:G2467S;ENSP00000349985:G2467S	ENSP00000349985:G2467S	G	+	1	0	VPS13A	79156162	1.000000	0.71417	0.993000	0.49108	0.754000	0.42855	7.778000	0.85637	2.563000	0.86464	0.555000	0.69702	GGT		0.473	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
AGTPBP1	23287	hgsc.bcm.edu	37	9	88247913	88247913	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:88247913A>G	ENST00000357081.3	-	14	1823	c.1679T>C	c.(1678-1680)cTt>cCt	p.L560P	AGTPBP1_ENST00000376109.3_Missense_Mutation_p.L572P|AGTPBP1_ENST00000432218.1_Missense_Mutation_p.L398P|AGTPBP1_ENST00000376083.3_Missense_Mutation_p.L520P|AGTPBP1_ENST00000337006.4_3'UTR			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	560					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						AGTAAGAGGAAGACTGCAGTC	0.433																																																	0			9											123.0	115.0	118.0					9																	88247913		2203	4300	6503	87437733	SO:0001583	missense	23287			AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 1"", ""tubulinyl-Tyr carboxypeptidase"", ""carboxypeptidase-tubulin"", ""tyrosine carboxypeptidase"", ""soluble carboxypeptidase"""	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.1679T>C	9.37:g.88247913A>G	ENSP00000349592:p.Leu560Pro		87437733	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Missense_Mutation	SNP	ENST00000357081.3	37		.	.	.	.	.	.	.	.	.	.	A	3.894	-0.023389	0.07634	.	.	ENSG00000135049	ENST00000357081;ENST00000376083;ENST00000376109;ENST00000432218	T;T;T;T	0.46063	2.21;2.21;2.18;0.88	5.93	3.45	0.39498	.	0.519691	0.19812	N	0.105516	T	0.15478	0.0373	N	0.03115	-0.41	0.09310	N	0.999994	B;B;B;B	0.10296	0.002;0.0;0.003;0.001	B;B;B;B	0.15484	0.001;0.001;0.013;0.001	T	0.05022	-1.0911	10	0.30854	T	0.27	-11.8214	1.2715	0.02022	0.3626:0.349:0.1186:0.1698	.	572;560;398;520	Q9UPW5-3;Q9UPW5;B4DHX2;Q9UPW5-2	.;CBPC1_HUMAN;.;.	P	560;520;572;398	ENSP00000349592:L560P;ENSP00000365251:L520P;ENSP00000365277:L572P;ENSP00000402804:L398P	ENSP00000349592:L560P	L	-	2	0	AGTPBP1	87437733	0.995000	0.38212	0.988000	0.46212	0.312000	0.27988	1.181000	0.32017	2.271000	0.75665	0.533000	0.62120	CTT		0.433	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239	
CDK20	23552	hgsc.bcm.edu	37	9	90582504	90582504	+	Missense_Mutation	SNP	C	C	T	rs376253655		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:90582504C>T	ENST00000325303.8	-	8	1219	c.914G>A	c.(913-915)cGt>cAt	p.R305H	CDK20_ENST00000605159.1_Missense_Mutation_p.V275I|CDK20_ENST00000336654.5_Missense_Mutation_p.R297H|CDK20_ENST00000375871.4_Missense_Mutation_p.V243I|CDK20_ENST00000375883.3_Missense_Mutation_p.R284H	NM_001039803.2	NP_001034892.1	Q8IZL9	CDK20_HUMAN	cyclin-dependent kinase 20	305					cell cycle (GO:0007049)|cell division (GO:0051301)|multicellular organismal development (GO:0007275)	cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			skin(1)	1						TCCCCCTAGACGCTGAGGAAT	0.612																																																	0			9						C	HIS/ARG,ILE/VAL,ILE/VAL,HIS/ARG,HIS/ARG	1,4267		0,1,2133	31.0	29.0	30.0		914,823,727,851,890	4.7	1.0	9		30	0,8326		0,0,4163	no	missense,missense,missense,missense,missense	CDK20	NM_001039803.2,NM_001170639.1,NM_001170640.1,NM_012119.4,NM_178432.3	29,29,29,29,29	0,1,6296	TT,TC,CC		0.0,0.0234,0.0079	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	305/347,275/276,243/244,284/326,297/339	90582504	1,12593	2134	4163	6297	89772324	SO:0001583	missense	0			AF035013	CCDS6677.1, CCDS6678.1, CCDS35060.1, CCDS55324.1, CCDS65075.1	9q22.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000156345	ENSG00000156345		"""Cyclin-dependent kinases"""	21420	protein-coding gene	gene with protein product		610076	"""cell cycle related kinase"""	CCRK		19884882	Standard	NM_178432		Approved	p42	uc004apr.3	Q8IZL9	OTTHUMG00000020161	ENST00000325303.8:c.914G>A	9.37:g.90582504C>T	ENSP00000322343:p.Arg305His		89772324	A2A389|A2A390|B4DQX1|O95137|Q5EDC4|Q5VYW1|Q9BUF4	Missense_Mutation	SNP	ENST00000325303.8	37	CCDS35060.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	23.7|23.7	4.446060|4.446060	0.84101|0.84101	2.34E-4|2.34E-4	0.0|0.0	ENSG00000156345|ENSG00000156345	ENST00000375883;ENST00000336654;ENST00000325303;ENST00000286878|ENST00000375871	T;T;T|T	0.69561|0.64438	-0.08;-0.24;-0.41|-0.1	4.7|4.7	4.7|4.7	0.59300|0.59300	Protein kinase-like domain (1);|.	0.065878|.	0.64402|.	D|.	0.000018|.	T|T	0.47377|0.47377	0.1442|0.1442	.|.	.|.	.|.	0.23636|0.23636	N|N	0.997237|0.997237	D;D;D|B	0.89917|0.30482	1.0;1.0;0.999|0.281	D;D;P|B	0.70935|0.19666	0.971;0.935;0.885|0.026	T|T	0.31530|0.31530	-0.9940|-0.9940	9|8	0.72032|0.30854	D|T	0.01|0.27	-17.2466|-17.2466	13.5185|13.5185	0.61553|0.61553	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	297;284;305|243	A2A390;E7EQ88;Q8IZL9|Q8IZL9-2	.;.;CDK20_HUMAN|.	H|I	284;297;305;284|243	ENSP00000365043:R284H;ENSP00000338975:R297H;ENSP00000322343:R305H|ENSP00000365031:V243I	ENSP00000286878:R284H|ENSP00000365031:V243I	R|V	-|-	2|1	0|0	CDK20|CDK20	89772324|89772324	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.785000|0.785000	0.44390|0.44390	4.951000|4.951000	0.63610|0.63610	2.335000|2.335000	0.79485|0.79485	0.561000|0.561000	0.74099|0.74099	CGT|GTC		0.612	CDK20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214996.1	NM_012119	
S1PR3	1903	hgsc.bcm.edu	37	9	91616968	91616968	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:91616968G>A	ENST00000375846.3	+	1	5548	c.853G>A	c.(853-855)Gtg>Atg	p.V285M	S1PR3_ENST00000358157.2_Missense_Mutation_p.V285M			Q99500	S1PR3_HUMAN	sphingosine-1-phosphate receptor 3	285					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|anatomical structure morphogenesis (GO:0009653)|cytokine production (GO:0001816)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of establishment of endothelial barrier (GO:1903141)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of interleukin-1 beta production (GO:0032651)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)	p.V285M(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(1)	34						GTGGTTCATCGTGTTGGCTGT	0.597																																																	1	Substitution - Missense(1)	endometrium(1)	9											119.0	73.0	89.0					9																	91616968		2203	4300	6503	90806788	SO:0001583	missense	1903			AF022139	CCDS6680.1	9q22.1-q22.2	2012-08-08	2008-04-30	2008-04-30	ENSG00000213694	ENSG00000213694		"""GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"""	3167	protein-coding gene	gene with protein product	"""sphingosine-1-phosphate receptor 3"""	601965	"""endothelial differentiation, sphingolipid G-protein-coupled receptor, 3"""	EDG3		8878560, 9409733	Standard	NM_005226		Approved	EDG-3	uc004aqe.4	Q99500	OTTHUMG00000020173	ENST00000375846.3:c.853G>A	9.37:g.91616968G>A	ENSP00000365006:p.Val285Met		90806788	Q5SQD8|Q7Z5I2	Missense_Mutation	SNP	ENST00000375846.3	37	CCDS6680.1	.	.	.	.	.	.	.	.	.	.	G	11.38	1.620387	0.28801	.	.	ENSG00000213694	ENST00000358157;ENST00000375846	T;T	0.72615	-0.67;-0.67	4.85	1.62	0.23740	GPCR, rhodopsin-like superfamily (1);	0.894418	0.09595	N	0.781019	T	0.60702	0.2289	L	0.46885	1.475	0.20764	N	0.999852	B	0.19817	0.039	B	0.14023	0.01	T	0.47548	-0.9109	10	0.34782	T	0.22	.	7.2013	0.25883	0.3589:0.0:0.6411:0.0	.	285	Q99500	S1PR3_HUMAN	M	285	ENSP00000350878:V285M;ENSP00000365006:V285M	ENSP00000350878:V285M	V	+	1	0	S1PR3	90806788	0.197000	0.23362	0.991000	0.47740	0.713000	0.41058	2.807000	0.47955	0.199000	0.20427	0.313000	0.20887	GTG		0.597	S1PR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052979.2	NM_005226	
SEMA4D	10507	hgsc.bcm.edu	37	9	91996163	91996163	+	Silent	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:91996163C>T	ENST00000450295.1	-	14	2321	c.1545G>A	c.(1543-1545)gcG>gcA	p.A515A	SEMA4D_ENST00000420987.1_Silent_p.A515A|SEMA4D_ENST00000438547.2_Silent_p.A515A|SEMA4D_ENST00000422704.2_Silent_p.A515A|SEMA4D_ENST00000455551.2_Silent_p.A515A|SEMA4D_ENST00000339861.4_Silent_p.A515A|SEMA4D_ENST00000356444.2_Silent_p.A515A|SEMA4D_ENST00000343780.4_Silent_p.A515A			Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	515	PSI.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						AGGGGTCCCGCGCCAGCACAC	0.687																																																	0			9											34.0	35.0	34.0					9																	91996163		2202	4299	6501	91185983	SO:0001819	synonymous_variant	10507			U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"""Semaphorins"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10732	protein-coding gene	gene with protein product	"""M-sema G"""	601866	"""chromosome 9 open reading frame 164"""	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000450295.1:c.1545G>A	9.37:g.91996163C>T			91185983	B2RPM6|Q7Z5S4|Q8N8B0	Silent	SNP	ENST00000450295.1	37	CCDS6685.1																																																																																				0.687	SEMA4D-018	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342411.1	NM_006378	
COL27A1	85301	hgsc.bcm.edu	37	9	117070032	117070032	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:117070032T>C	ENST00000356083.3	+	59	5582	c.5191T>C	c.(5191-5193)Tgt>Cgt	p.C1731R		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1731	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						TGGACAGACGTGTCTCAAGCC	0.607																																																	0			9											212.0	156.0	175.0					9																	117070032		2203	4300	6503	116109853	SO:0001583	missense	85301			AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.5191T>C	9.37:g.117070032T>C	ENSP00000348385:p.Cys1731Arg		116109853	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	T	16.60	3.167610	0.57476	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.88046	-2.33	5.6	4.46	0.54185	Fibrillar collagen, C-terminal (3);	.	.	.	.	D	0.95262	0.8463	H	0.96633	3.855	0.80722	D	1	D;D	0.89917	1.0;0.983	D;D	0.97110	1.0;0.924	D	0.95146	0.8268	9	0.62326	D	0.03	.	11.0616	0.47950	0.0:0.0:0.156:0.844	.	46;1731	Q9HAA3;Q8IZC6	.;CORA1_HUMAN	R	1731;1738	ENSP00000348385:C1731R	ENSP00000348385:C1731R	C	+	1	0	COL27A1	116109853	1.000000	0.71417	0.968000	0.41197	0.965000	0.64279	6.293000	0.72731	0.947000	0.37659	0.459000	0.35465	TGT		0.607	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
COL5A1	1289	hgsc.bcm.edu	37	9	137622201	137622201	+	Silent	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:137622201G>A	ENST00000371817.3	+	7	1458	c.1044G>A	c.(1042-1044)acG>acA	p.T348T		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	348	Nonhelical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)	p.T348T(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		ACTACTACACGCCCTCACCGT	0.632																																																	1	Substitution - coding silent(1)	large_intestine(1)	9											126.0	114.0	118.0					9																	137622201		2203	4300	6503	136762022	SO:0001819	synonymous_variant	1289			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.1044G>A	9.37:g.137622201G>A			136762022	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																				0.632	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
NOTCH1	4851	hgsc.bcm.edu	37	9	139390675	139390675	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr9:139390675C>A	ENST00000277541.6	-	34	7591	c.7516G>T	c.(7516-7518)Gag>Tag	p.E2506*		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2506					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E2507*(1)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		AAGGGGTGCTCAGGCACCTGT	0.682			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)																														Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	9											20.0	28.0	25.0					9																	139390675		2098	4192	6290	138510496	SO:0001587	stop_gained	4851			AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.7516G>T	9.37:g.139390675C>A	ENSP00000277541:p.Glu2506*		138510496	Q59ED8|Q5SXM3	Nonsense_Mutation	SNP	ENST00000277541.6	37	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	C	48	14.592525	0.99802	.	.	ENSG00000148400	ENST00000277541	.	.	.	5.24	5.24	0.73138	.	0.050760	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	18.1647	0.89721	0.0:1.0:0.0:0.0	.	.	.	.	X	2506	.	ENSP00000277541:E2506X	E	-	1	0	NOTCH1	138510496	1.000000	0.71417	0.995000	0.50966	0.954000	0.61252	7.664000	0.83830	2.616000	0.88540	0.462000	0.41574	GAG		0.682	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
LATS2	26524	hgsc.bcm.edu	37	13	21549228	21549228	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr13:21549228T>C	ENST00000382592.4	-	8	3453	c.3048A>G	c.(3046-3048)gaA>gaG	p.E1016E	LATS2_ENST00000542899.1_Silent_p.E1016E	NM_014572.2	NP_055387.2			large tumor suppressor kinase 2											breast(4)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(2)	45		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		TGGTGCTACCTTCGCTGGCAT	0.542																																																	0			13											253.0	221.0	232.0					13																	21549228		2203	4300	6503	20447228	SO:0001819	synonymous_variant	26524			AB028019	CCDS9294.1	13q11-q12	2013-04-25	2013-04-25		ENSG00000150457	ENSG00000150457			6515	protein-coding gene	gene with protein product		604861	"""LATS (large tumor suppressor, Drosophila) homolog 2"", ""LATS, large tumor suppressor, homolog 2 (Drosophila)"""			10673337	Standard	NM_014572		Approved		uc001unr.4	Q9NRM7	OTTHUMG00000016531	ENST00000382592.4:c.3048A>G	13.37:g.21549228T>C			20447228		Silent	SNP	ENST00000382592.4	37	CCDS9294.1																																																																																				0.542	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1		
PROSER1	80209	hgsc.bcm.edu	37	13	39587388	39587388	+	Silent	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr13:39587388A>G	ENST00000352251.3	-	11	2834	c.2001T>C	c.(1999-2001)agT>agC	p.S667S	PROSER1_ENST00000350125.3_Silent_p.S645S|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	667	Ser-rich.																TTAAAGGAGTACTCAAGCTGG	0.458																																																	0			13											123.0	115.0	117.0					13																	39587388		2203	4300	6503	38485388	SO:0001819	synonymous_variant	80209			AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 23"""	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.2001T>C	13.37:g.39587388A>G			38485388	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Silent	SNP	ENST00000352251.3	37	CCDS9368.2																																																																																				0.458	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138	
RB1	5925	hgsc.bcm.edu	37	13	48951109	48951109	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr13:48951109A>G	ENST00000267163.4	+	13	1409	c.1271A>G	c.(1270-1272)tAc>tGc	p.Y424C		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	424	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	GATATAGGATACATCTTTAAA	0.358		6	"""D, Mis, N, F, S"""		"""retinoblastoma, sarcoma, breast, small cell lung"""	"""retinoblastoma, sarcoma, breast, small cell lung"""			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																													yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"""L, E, M, O"""	23	Whole gene deletion(15)|Unknown(8)	bone(11)|breast(5)|central_nervous_system(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	13											109.0	117.0	115.0					13																	48951109		2203	4299	6502	47849110	SO:0001583	missense	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"""Endogenous ligands"""	9884	protein-coding gene	gene with protein product	"""prepro-retinoblastoma-associated protein"", ""protein phosphatase 1, regulatory subunit 130"""	614041	"""osteosarcoma"""	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1271A>G	13.37:g.48951109A>G	ENSP00000267163:p.Tyr424Cys		47849110	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	A	10.40	1.338827	0.24253	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.87650	-2.28	5.93	-1.42	0.08913	Retinoblastoma-associated protein, A-box (1);Cyclin-like (2);	1.054330	0.07280	N	0.870674	T	0.72431	0.3459	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.55805	-0.8083	10	0.37606	T	0.19	.	7.6705	0.28455	0.4623:0.0:0.4311:0.1067	.	424	P06400	RB_HUMAN	C	403;424	ENSP00000267163:Y424C	ENSP00000267163:Y424C	Y	+	2	0	RB1	47849110	0.282000	0.24268	0.050000	0.19076	0.982000	0.71751	1.045000	0.30341	-0.633000	0.05545	0.482000	0.46254	TAC		0.358	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		
TDRD3	81550	hgsc.bcm.edu	37	13	61084006	61084006	+	Missense_Mutation	SNP	T	T	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr13:61084006T>A	ENST00000196169.3	+	9	1477	c.689T>A	c.(688-690)cTt>cAt	p.L230H	TDRD3_ENST00000377881.2_Missense_Mutation_p.L230H|TDRD3_ENST00000377894.2_Missense_Mutation_p.L230H|TDRD3_ENST00000535286.1_Missense_Mutation_p.L323H	NM_001146071.1|NM_030794.2	NP_001139543.1|NP_110421.1	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3	230	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				chromatin modification (GO:0016568)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	40		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		CTGAACGTACTTCTTACAAGC	0.403																																					Colon(36;164 906 35820 50723)												0			13											124.0	118.0	120.0					13																	61084006		2203	4300	6503	59982007	SO:0001583	missense	81550			AK023578	CCDS9441.1, CCDS53872.1	13q14.3	2013-01-23			ENSG00000083544	ENSG00000083544		"""Tudor domain containing"""	20612	protein-coding gene	gene with protein product		614392					Standard	NM_030794		Approved	FLJ21007	uc010aeg.3	Q9H7E2	OTTHUMG00000017007	ENST00000196169.3:c.689T>A	13.37:g.61084006T>A	ENSP00000196169:p.Leu230His		59982007	B2MWP9|Q53XA6|Q6P992	Missense_Mutation	SNP	ENST00000196169.3	37	CCDS9441.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.327256	0.81690	.	.	ENSG00000083544	ENST00000196169;ENST00000377881;ENST00000377894;ENST00000535286	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	5.99	5.99	0.97316	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1);	0.000000	0.85682	D	0.000000	T	0.78978	0.4369	M	0.72353	2.195	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.81070	-0.1099	10	0.87932	D	0	-18.2117	16.4943	0.84223	0.0:0.0:0.0:1.0	.	323;229;230	Q9H7E2-3;Q9H7E2-2;Q9H7E2	.;.;TDRD3_HUMAN	H	230;230;230;323	ENSP00000196169:L230H;ENSP00000367113:L230H;ENSP00000367126:L230H;ENSP00000440190:L323H	ENSP00000196169:L230H	L	+	2	0	TDRD3	59982007	1.000000	0.71417	0.999000	0.59377	0.723000	0.41478	7.474000	0.81024	2.291000	0.77112	0.533000	0.62120	CTT		0.403	TDRD3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045175.2	NM_030794	
CDC123	8872	hgsc.bcm.edu	37	10	12291612	12291612	+	Silent	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:12291612A>G	ENST00000281141.4	+	12	1159	c.879A>G	c.(877-879)gaA>gaG	p.E293E	RP11-186N15.3_ENST00000421657.1_RNA|CDC123_ENST00000455773.3_3'UTR|CDC123_ENST00000378900.2_Silent_p.E252E	NM_006023.2	NP_006014.2	O75794	CD123_HUMAN	cell division cycle 123	293					cell cycle arrest (GO:0007050)|cell division (GO:0051301)|positive regulation of cell proliferation (GO:0008284)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12						CAAACAGTGAAGTGACAGTCC	0.433																																																	0			10											112.0	103.0	106.0					10																	12291612		2203	4300	6503	12331618	SO:0001819	synonymous_variant	8872			BC001600	CCDS7090.1	10p13	2013-01-17	2013-01-17	2006-11-06	ENSG00000151465	ENSG00000151465			16827	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 7"", ""cell division cycle 123 homolog (S. cerevisiae)"""	C10orf7		15319434	Standard	NM_006023		Approved	D123	uc001ill.3	O75794	OTTHUMG00000017680	ENST00000281141.4:c.879A>G	10.37:g.12291612A>G			12331618	A8JZZ7|Q14107|Q5T0L4|Q5T0L5|Q5T0L7|Q5T0L8|Q5T0L9	Silent	SNP	ENST00000281141.4	37	CCDS7090.1																																																																																				0.433	CDC123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046801.1	NM_006023	
FAM107B	83641	hgsc.bcm.edu	37	10	14563961	14563961	+	Silent	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:14563961T>C	ENST00000378470.1	-	3	472	c.186A>G	c.(184-186)cgA>cgG	p.R62R	FAM107B_ENST00000181796.2_Silent_p.R237R|FAM107B_ENST00000378465.3_Silent_p.R62R|FAM107B_ENST00000378462.1_Silent_p.R62R|FAM107B_ENST00000378467.4_Silent_p.R62R|FAM107B_ENST00000378458.2_Silent_p.R62R|FAM107B_ENST00000496330.1_Silent_p.R62R|FAM107B_ENST00000478076.1_Silent_p.R62R|FAM107B_ENST00000468747.1_Silent_p.R62R|FAM107B_ENST00000479731.1_Silent_p.R62R	NM_001282695.1|NM_001282696.1|NM_001282697.1|NM_001282698.1|NM_001282700.1|NM_001282701.1|NM_001282702.1|NM_001282703.1	NP_001269624.1|NP_001269625.1|NP_001269626.1|NP_001269627.1|NP_001269629.1|NP_001269630.1|NP_001269631.1|NP_001269632.1	Q9H098	F107B_HUMAN	family with sequence similarity 107, member B	62					sensory perception of sound (GO:0007605)					breast(7)|kidney(1)|large_intestine(4)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TTACTTGGTCTCGTTTTCTTT	0.398																																																	0			10											189.0	177.0	181.0					10																	14563961		2203	4300	6503	14603967	SO:0001819	synonymous_variant	83641			AK127413	CCDS7102.1, CCDS60486.1	10p14	2006-01-17	2006-01-17	2005-11-20	ENSG00000065809	ENSG00000065809			23726	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 45"""	C10orf45		11230166	Standard	XM_005252616		Approved	FLJ45505, MGC11034	uc001ina.1	Q9H098	OTTHUMG00000017709	ENST00000378470.1:c.186A>G	10.37:g.14563961T>C			14603967	A8K1P4|D3DRT2|Q5T9K7|Q5T9K8|Q6ZSI4	Silent	SNP	ENST00000378470.1	37																																																																																					0.398	FAM107B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046899.1	NM_031453	
PTCHD3	374308	hgsc.bcm.edu	37	10	27687573	27687573	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:27687573C>T	ENST00000438700.3	-	4	2071	c.1954G>A	c.(1954-1956)Gat>Aat	p.D652N		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	652					spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						GGACCATAATCTGAAAAATAA	0.358																																																	0			10											58.0	57.0	58.0					10																	27687573		2203	4300	6503	27727579	SO:0001583	missense	374308			AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.1954G>A	10.37:g.27687573C>T	ENSP00000417658:p.Asp652Asn		27727579	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	37	CCDS31173.1	.	.	.	.	.	.	.	.	.	.	C	10.48	1.362020	0.24684	.	.	ENSG00000182077	ENST00000438700	D	0.84944	-1.92	4.19	-0.192	0.13248	.	1.226220	0.05626	N	0.580749	T	0.78155	0.4239	L	0.39633	1.23	0.09310	N	1	B	0.23249	0.082	B	0.29663	0.105	T	0.57997	-0.7714	10	0.18710	T	0.47	-0.0831	5.9062	0.19002	0.0:0.449:0.308:0.243	.	652	Q3KNS1	PTHD3_HUMAN	N	652	ENSP00000417658:D652N	ENSP00000417658:D652N	D	-	1	0	PTCHD3	27727579	0.020000	0.18652	0.014000	0.15608	0.770000	0.43624	1.126000	0.31344	-0.246000	0.09611	0.484000	0.47621	GAT		0.358	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
ZNF33A	7581	hgsc.bcm.edu	37	10	38345270	38345270	+	Nonsense_Mutation	SNP	C	C	T	rs267602486		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:38345270C>T	ENST00000458705.2	+	5	2373	c.2215C>T	c.(2215-2217)Cag>Tag	p.Q739*	ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000374618.3_Nonsense_Mutation_p.Q740*|ZNF33A_ENST00000432900.2_Nonsense_Mutation_p.Q746*|ZNF33A_ENST00000307441.9_Nonsense_Mutation_p.Q739*			Q06730	ZN33A_HUMAN	zinc finger protein 33A	739					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q739*(1)		cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						TGCTCAACATCAGAGATCACA	0.388																																																	1	Substitution - Nonsense(1)	skin(1)	10											105.0	100.0	102.0					10																	38345270		2203	4300	6503	38385276	SO:0001587	stop_gained	7581			D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"""Zinc fingers, C2H2-type"", ""-"""	13096	protein-coding gene	gene with protein product	"""zinc finger and ZAK associated protein with KRAB domain"""	194521	"""zinc finger protein 33a (KOX 31)"", ""zinc finger protein 11A"""	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.2215C>T	10.37:g.38345270C>T	ENSP00000387713:p.Gln739*		38385276	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Nonsense_Mutation	SNP	ENST00000458705.2	37	CCDS31182.1	.	.	.	.	.	.	.	.	.	.	C	16.11	3.028792	0.54790	.	.	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	.	.	.	1.92	1.92	0.25849	.	0.000000	0.32343	N	0.006233	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	9.4078	0.38473	0.0:1.0:0.0:0.0	.	.	.	.	X	740;746;739;739	.	ENSP00000304268:Q739X	Q	+	1	0	ZNF33A	38385276	0.000000	0.05858	0.993000	0.49108	0.337000	0.28794	0.276000	0.18716	1.044000	0.40200	0.313000	0.20887	CAG		0.388	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
AGAP4	119016	hgsc.bcm.edu	37	10	46321475	46321475	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:46321475A>G	ENST00000448048.2	-	7	2005	c.1880T>C	c.(1879-1881)gTc>gCc	p.V627A	AGAP4_ENST00000430779.2_5'Flank	NM_133446.2	NP_597703.2	Q96P64	AGAP4_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 4	627					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			central_nervous_system(1)|lung(1)|ovary(1)	3						TCGGGCCATGACGTCCACCCC	0.672																																																	0			10											1.0	1.0	1.0					10																	46321475		216	377	593	45641481	SO:0001583	missense	119016			AF411132	CCDS7215.1	10q11.21	2014-06-19	2008-09-22	2008-09-22	ENSG00000188234	ENSG00000188234		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	23459	protein-coding gene	gene with protein product			"""centaurin, gamma-like family, member 1"", ""ArfGAP with GTPase domain, ankyrin repeat and PH domain 8"", ""centaurin, gamma-like family, member 5"""	CTGLF1, AGAP8, CTGLF5		12477932	Standard	XM_005271797		Approved	Em:AC012044.1, MRIP2	uc001jcx.4	Q96P64	OTTHUMG00000018088	ENST00000448048.2:c.1880T>C	10.37:g.46321475A>G	ENSP00000392513:p.Val627Ala		45641481		Missense_Mutation	SNP	ENST00000448048.2	37	CCDS7215.1	.	.	.	.	.	.	.	.	.	.	a	9.177	1.022587	0.19433	.	.	ENSG00000188234	ENST00000448048;ENST00000342551	T	0.68479	-0.33	.	.	.	Ankyrin repeat-containing domain (4);	0.223555	0.38436	N	0.001698	T	0.47967	0.1474	L	0.31294	0.92	0.27716	N	0.945282	B;B	0.15141	0.012;0.007	B;B	0.23150	0.044;0.029	T	0.37361	-0.9709	9	0.52906	T	0.07	.	4.5362	0.12032	0.9994:0.0:6.0E-4:0.0	.	650;627	C9JRW4;Q96P64	.;AGAP4_HUMAN	A	627;403	ENSP00000392513:V627A	ENSP00000343438:V403A	V	-	2	0	AGAP4	45641481	0.987000	0.35691	0.263000	0.24496	0.266000	0.26442	6.064000	0.71169	0.093000	0.17368	0.092000	0.15492	GTC		0.672	AGAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047799.1	NM_133446	
PTEN	5728	hgsc.bcm.edu	37	10	89720711	89720711	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:89720711G>A	ENST00000371953.3	+	8	2219	c.862G>A	c.(862-864)Gaa>Aaa	p.E288K	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	288	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.E288*(2)|p.G165_*404del(1)|p.S287fs*8(1)|p.W274_F341del(1)|p.S287fs*1(1)|p.E288K(1)|p.E288fs*9(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		GGAAACCTCAGAAAAAGTAGA	0.313		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																													yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	56	Whole gene deletion(37)|Deletion - Frameshift(12)|Deletion - In frame(2)|Substitution - Nonsense(2)|Unknown(2)|Substitution - Missense(1)	prostate(16)|central_nervous_system(12)|skin(6)|endometrium(4)|lung(4)|ovary(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|urinary_tract(2)|vulva(1)|soft_tissue(1)	10											56.0	59.0	58.0					10																	89720711		2202	4296	6498	89710691	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.862G>A	10.37:g.89720711G>A	ENSP00000361021:p.Glu288Lys		89710691	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	17.15	3.317240	0.60524	.	.	ENSG00000171862	ENST00000371953	D	0.84800	-1.9	5.13	5.13	0.70059	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.146381	0.64402	D	0.000011	T	0.78451	0.4285	N	0.24115	0.695	0.58432	D	0.999999	B	0.23185	0.081	B	0.28385	0.089	T	0.72646	-0.4230	9	.	.	.	-13.8205	18.5632	0.91108	0.0:0.0:1.0:0.0	.	288	P60484	PTEN_HUMAN	K	288	ENSP00000361021:E288K	.	E	+	1	0	PTEN	89710691	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.369000	0.97156	2.399000	0.81585	0.591000	0.81541	GAA		0.313	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
PTEN	5728	hgsc.bcm.edu	37	10	89720745	89720745	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:89720745A>G	ENST00000371953.3	+	8	2253	c.896A>G	c.(895-897)gAa>gGa	p.E299G	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	299	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.W274_F341del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TGTGATCAAGAAATCGATAGC	0.328		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																													yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	50	Whole gene deletion(37)|Deletion - Frameshift(9)|Deletion - In frame(2)|Unknown(2)	prostate(16)|central_nervous_system(12)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	10											95.0	93.0	94.0					10																	89720745		2203	4298	6501	89710725	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.896A>G	10.37:g.89720745A>G	ENSP00000361021:p.Glu299Gly		89710725	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	18.53	3.643976	0.67244	.	.	ENSG00000171862	ENST00000371953	D	0.94828	-3.53	5.13	5.13	0.70059	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.222866	0.46442	D	0.000294	D	0.90463	0.7013	L	0.36672	1.1	0.58432	D	0.999997	B	0.02656	0.0	B	0.04013	0.001	D	0.86672	0.1911	9	.	.	.	-14.8198	14.9228	0.70854	1.0:0.0:0.0:0.0	.	299	P60484	PTEN_HUMAN	G	299	ENSP00000361021:E299G	.	E	+	2	0	PTEN	89710725	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.724000	0.61972	1.942000	0.56320	0.482000	0.46254	GAA		0.328	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
STAMBPL1	57559	hgsc.bcm.edu	37	10	90676486	90676486	+	Missense_Mutation	SNP	C	C	T	rs140820995	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:90676486C>T	ENST00000371926.3	+	8	1911	c.953C>T	c.(952-954)gCg>gTg	p.A318V	STAMBPL1_ENST00000371924.1_Missense_Mutation_p.A318V|STAMBPL1_ENST00000371922.1_Missense_Mutation_p.A152V|STAMBPL1_ENST00000371927.3_Missense_Mutation_p.A318V	NM_020799.3	NP_065850.1	Q96FJ0	STALP_HUMAN	STAM binding protein-like 1	318	MPN.					membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)	p.A318E(1)		breast(2)|endometrium(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(1)	11		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)		AAGCAGTCTGCGGGACCAGAC	0.373																																																	1	Substitution - Missense(1)	ovary(1)	10						C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	163.0	151.0	155.0		953	6.1	1.0	10	dbSNP_134	155	7,8593	5.7+/-21.5	0,7,4293	yes	missense	STAMBPL1	NM_020799.2	64	0,8,6495	TT,TC,CC		0.0814,0.0227,0.0615	probably-damaging	318/437	90676486	8,12998	2203	4300	6503	90666466	SO:0001583	missense	57559			AB037794	CCDS7391.1	10q23.32	2006-11-08			ENSG00000138134	ENSG00000138134			24105	protein-coding gene	gene with protein product	"""associated molecule with the SH3 domain of STAM (AMSH) like protein"", ""associated molecule with the SH3 domain of STAM (AMSH) - Family Protein"""	612352				12810066, 12943674	Standard	NM_020799		Approved	AMSH-LP, KIAA1373, AMSH-FP, FLJ31524, ALMalpha, bA399O19.2	uc001kfk.4	Q96FJ0	OTTHUMG00000018702	ENST00000371926.3:c.953C>T	10.37:g.90676486C>T	ENSP00000360994:p.Ala318Val		90666466	B3KPA7|Q5T9N4|Q5T9N9|Q7Z420|Q9P2H4	Missense_Mutation	SNP	ENST00000371926.3	37	CCDS7391.1	.	.	.	.	.	.	.	.	.	.	C	18.90	3.720747	0.68959	2.27E-4	8.14E-4	ENSG00000138134	ENST00000371926;ENST00000371927;ENST00000371924;ENST00000371922	T;T;T;T	0.55234	0.53;0.53;0.53;0.53	6.07	6.07	0.98685	.	0.065128	0.64402	D	0.000014	T	0.43765	0.1262	L	0.53561	1.675	0.38881	D	0.956903	P;D	0.61697	0.863;0.99	B;B	0.32762	0.052;0.152	T	0.57659	-0.7773	10	0.72032	D	0.01	-3.199	14.7776	0.69740	0.0:0.8559:0.1441:0.0	.	318;318	Q96FJ0-2;Q96FJ0	.;STALP_HUMAN	V	318;318;318;152	ENSP00000360994:A318V;ENSP00000360995:A318V;ENSP00000360992:A318V;ENSP00000360990:A152V	ENSP00000360990:A152V	A	+	2	0	STAMBPL1	90666466	0.999000	0.42202	0.973000	0.42090	0.988000	0.76386	3.946000	0.56644	2.885000	0.99019	0.650000	0.86243	GCG		0.373	STAMBPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049283.1	NM_020799	
CYP2C19	1557	hgsc.bcm.edu	37	10	96535288	96535288	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:96535288A>G	ENST00000371321.3	+	3	555	c.473A>G	c.(472-474)aAa>aGa	p.K158R	CYP2C19_ENST00000464755.1_3'UTR	NM_000769.1	NP_000760	P33261	CP2CJ_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 19	158					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	43		Colorectal(252;0.09)		all cancers(201;6.02e-07)|KIRC - Kidney renal clear cell carcinoma(50;0.0672)|Kidney(138;0.0838)	Acenocoumarol(DB01418)|Acetylsalicylic acid(DB00945)|Adinazolam(DB00546)|Almotriptan(DB00918)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amoxicillin(DB01060)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Benzatropine(DB00245)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bortezomib(DB00188)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carisoprodol(DB00395)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clevidipine(DB04920)|Clobazam(DB00349)|Clomipramine(DB01242)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enfuvirtide(DB00109)|Enzalutamide(DB08899)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estradiol(DB00783)|Ethanol(DB00898)|Ethotoin(DB00754)|Etoricoxib(DB01628)|Etravirine(DB06414)|Famotidine(DB00927)|Felbamate(DB00949)|Fluconazole(DB00196)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Gliclazide(DB01120)|Glucosamine(DB01296)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Hexobarbital(DB01355)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Indomethacin(DB00328)|Isoniazid(DB00951)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumiracoxib(DB01283)|MACITENTAN(DB08932)|Melatonin(DB01065)|Memantine(DB01043)|Meprobamate(DB00371)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methsuximide(DB05246)|Methylphenobarbital(DB00849)|Metoprolol(DB00264)|Miconazole(DB01110)|Moclobemide(DB01171)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Nicotine(DB00184)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Norethindrone(DB00717)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ospemifene(DB04938)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Pantoprazole(DB00213)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phensuximide(DB00832)|Phenytoin(DB00252)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Prasugrel(DB06209)|Praziquantel(DB01058)|Prednisone(DB00635)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propofol(DB00818)|Propranolol(DB00571)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Telmisartan(DB00966)|Temazepam(DB00231)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Timolol(DB00373)|Tioconazole(DB01007)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tolbutamide(DB01124)|Tolterodine(DB01036)|Topiramate(DB00273)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zolpidem(DB00425)|Zonisamide(DB00909)	GAGTTGAGAAAAACCAAGGGT	0.507																																																	0			10											159.0	154.0	156.0					10																	96535288		2203	4300	6503	96525278	SO:0001583	missense	1557			M61854	CCDS7436.1	10q24	2007-12-14	2003-01-14		ENSG00000165841	ENSG00000165841		"""Cytochrome P450s"""	2621	protein-coding gene	gene with protein product		124020	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 19"""	CYP2C		2009263, 8530044	Standard	NM_000769		Approved	P450IIC19, CPCJ	uc010qnz.2	P33261	OTTHUMG00000018799	ENST00000371321.3:c.473A>G	10.37:g.96535288A>G	ENSP00000360372:p.Lys158Arg		96525278	P33259|Q8WZB1|Q8WZB2|Q9UCD4	Missense_Mutation	SNP	ENST00000371321.3	37	CCDS7436.1	.	.	.	.	.	.	.	.	.	.	A	12.78	2.040661	0.35989	.	.	ENSG00000165841	ENST00000371321	T	0.70516	-0.49	3.9	2.71	0.32032	.	0.699906	0.12222	U	0.488301	T	0.73853	0.3640	M	0.63169	1.94	0.09310	N	1	P	0.45569	0.861	P	0.51079	0.658	T	0.62793	-0.6779	10	0.87932	D	0	.	7.8523	0.29462	0.8935:0.0:0.1065:0.0	.	158	P33261	CP2CJ_HUMAN	R	158	ENSP00000360372:K158R	ENSP00000360372:K158R	K	+	2	0	CYP2C19	96525278	0.000000	0.05858	0.129000	0.21949	0.444000	0.32077	0.278000	0.18753	0.466000	0.27193	0.333000	0.21579	AAA		0.507	CYP2C19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049490.1	NM_000769	
TAF5	6877	hgsc.bcm.edu	37	10	105138095	105138095	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:105138095C>T	ENST00000369839.3	+	3	924	c.901C>T	c.(901-903)Cga>Tga	p.R301*	TAF5_ENST00000351396.4_Nonsense_Mutation_p.R301*	NM_006951.3	NP_008882.2	Q15542	TAF5_HUMAN	TAF5 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 100kDa	301					chromatin modification (GO:0016568)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	protein dimerization activity (GO:0046983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)	15		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;1.83e-09)|all cancers(201;1.4e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		GTTGGATTTTCGAACAAGTAA	0.398																																																	0			10											137.0	127.0	130.0					10																	105138095		2203	4300	6503	105128085	SO:0001587	stop_gained	6877			X95525	CCDS7547.1	10q24-q25.2	2013-01-10	2002-08-29	2001-12-07	ENSG00000148835	ENSG00000148835		"""WD repeat domain containing"""	11539	protein-coding gene	gene with protein product		601787	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, D, 100kD"""	TAF2D		8884287, 8942982	Standard	NM_006951		Approved	TAFII100	uc001kwv.3	Q15542	OTTHUMG00000018985	ENST00000369839.3:c.901C>T	10.37:g.105138095C>T	ENSP00000358854:p.Arg301*		105128085	A8K5B4|B2RMR0|B7ZKJ6|Q53EM4|Q5SYD5|Q86UZ7|Q9Y4K5	Nonsense_Mutation	SNP	ENST00000369839.3	37	CCDS7547.1	.	.	.	.	.	.	.	.	.	.	C	36	5.860507	0.97036	.	.	ENSG00000148835	ENST00000369839;ENST00000351396	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.7494	19.8062	0.96532	0.0:1.0:0.0:0.0	.	.	.	.	X	301	.	ENSP00000311024:R301X	R	+	1	2	TAF5	105128085	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.781000	0.68964	2.676000	0.91093	0.555000	0.69702	CGA		0.398	TAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050144.1		
VWA2	340706	hgsc.bcm.edu	37	10	116032537	116032537	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:116032537T>C	ENST00000392982.3	+	6	660	c.410T>C	c.(409-411)cTt>cCt	p.L137P	VWA2_ENST00000603594.1_Missense_Mutation_p.L137P			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	137	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.		L -> R (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)	p.L137R(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		CTGAAATACCTTCTGCACAGA	0.537																																																	1	Substitution - Missense(1)	large_intestine(1)	10											112.0	109.0	110.0					10																	116032537		2203	4300	6503	116022527	SO:0001583	missense	340706			AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.410T>C	10.37:g.116032537T>C	ENSP00000376708:p.Leu137Pro		116022527	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	37		.	.	.	.	.	.	.	.	.	.	T	14.42	2.530212	0.45073	.	.	ENSG00000165816	ENST00000392982;ENST00000298715	D	0.83837	-1.77	4.83	3.67	0.42095	von Willebrand factor, type A (3);	0.341394	0.27323	N	0.019887	D	0.90099	0.6907	M	0.87547	2.89	0.53005	D	0.999964	D;D	0.69078	0.997;0.996	D;D	0.67103	0.949;0.914	D	0.88651	0.3182	10	0.48119	T	0.1	.	9.2493	0.37545	0.1612:0.0:0.0:0.8388	.	137;137	Q5GFL6;Q5GFL6-2	VWA2_HUMAN;.	P	137	ENSP00000376708:L137P	ENSP00000298715:L137P	L	+	2	0	VWA2	116022527	1.000000	0.71417	0.998000	0.56505	0.371000	0.29859	5.402000	0.66332	0.656000	0.30886	0.533000	0.62120	CTT		0.537	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496	
FGFR2	2263	hgsc.bcm.edu	37	10	123263319	123263319	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:123263319T>C	ENST00000358487.5	-	10	1696	c.1424A>G	c.(1423-1425)gAg>gGg	p.E475G	FGFR2_ENST00000360144.3_Missense_Mutation_p.E387G|FGFR2_ENST00000351936.6_Missense_Mutation_p.E473G|FGFR2_ENST00000369061.4_Missense_Mutation_p.E363G|FGFR2_ENST00000357555.5_Missense_Mutation_p.E386G|FGFR2_ENST00000356226.4_Missense_Mutation_p.E358G|FGFR2_ENST00000369056.1_Missense_Mutation_p.E476G|FGFR2_ENST00000457416.2_Missense_Mutation_p.E476G|FGFR2_ENST00000346997.2_Missense_Mutation_p.E473G|FGFR2_ENST00000369060.4_Missense_Mutation_p.E359G|FGFR2_ENST00000369059.1_Missense_Mutation_p.E361G|FGFR2_ENST00000478859.1_Missense_Mutation_p.E247G	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	475					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	TCTTGGAAACTCCCATTTTGG	0.488		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome																															Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	0			10											76.0	75.0	76.0					10																	123263319		2203	4300	6503	123253309	SO:0001583	missense	2263	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.1424A>G	10.37:g.123263319T>C	ENSP00000351276:p.Glu475Gly		123253309	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Missense_Mutation	SNP	ENST00000358487.5	37	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.837995	0.91117	.	.	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369060;ENST00000369059;ENST00000429361;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91843	-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92	6.03	6.03	0.97812	Protein kinase-like domain (1);	0.043220	0.85682	D	0.000000	D	0.96700	0.8923	M	0.88450	2.955	0.80722	D	1	D;D;D;P;D;D;D;P	0.89917	0.997;0.999;1.0;0.887;1.0;0.999;1.0;0.826	P;D;D;P;D;D;D;B	0.97110	0.885;0.946;1.0;0.561;0.931;0.946;0.987;0.282	D	0.97317	0.9941	10	0.87932	D	0	.	16.5655	0.84588	0.0:0.0:0.0:1.0	.	492;474;386;358;475;387;476;378	D3DRD5;P21802-18;P21802-21;P21802-20;P21802;P21802-22;P21802-17;D3DRD3	.;.;.;.;FGFR2_HUMAN;.;.;.	G	386;476;363;475;358;359;361;67;473;476;473;387;476;476;384	ENSP00000350166:E386G;ENSP00000358057:E363G;ENSP00000351276:E475G;ENSP00000348559:E358G;ENSP00000358056:E359G;ENSP00000358055:E361G;ENSP00000404219:E67G;ENSP00000263451:E473G;ENSP00000410294:E476G;ENSP00000309878:E473G;ENSP00000353262:E387G;ENSP00000358052:E476G;ENSP00000358054:E476G;ENSP00000337665:E384G	ENSP00000337665:E384G	E	-	2	0	FGFR2	123253309	1.000000	0.71417	0.996000	0.52242	0.961000	0.63080	7.985000	0.88162	2.302000	0.77476	0.533000	0.62120	GAG		0.488	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141	
MKI67	4288	hgsc.bcm.edu	37	10	129901237	129901237	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:129901237A>G	ENST00000368654.3	-	13	9242	c.8867T>C	c.(8866-8868)cTa>cCa	p.L2956P	MKI67_ENST00000368653.3_Missense_Mutation_p.L2596P	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2956					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GGATATTTTTAGAGGTTTTCC	0.483																																																	0			10											90.0	97.0	94.0					10																	129901237		2203	4300	6503	129791227	SO:0001583	missense	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.8867T>C	10.37:g.129901237A>G	ENSP00000357643:p.Leu2956Pro		129791227	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	A	13.14	2.147707	0.37923	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.01981	4.55;4.52	3.91	-3.12	0.05282	.	1.287800	0.06003	N	0.648194	T	0.03695	0.0105	L	0.27053	0.805	0.09310	N	0.999996	B;D;D	0.89917	0.101;0.998;1.0	B;D;D	0.71184	0.046;0.962;0.972	T	0.36163	-0.9759	10	0.25751	T	0.34	.	0.2359	0.00186	0.3813:0.1613:0.2314:0.226	.	2955;2596;2956	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	P	2956;2596;2955	ENSP00000357643:L2956P;ENSP00000357642:L2596P	ENSP00000357642:L2596P	L	-	2	0	MKI67	129791227	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-1.006000	0.03671	-0.490000	0.06707	-0.379000	0.06801	CTA		0.483	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
ADCY2	108	hgsc.bcm.edu	37	5	7520992	7520992	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:7520992A>G	ENST00000338316.4	+	3	639	c.550A>G	c.(550-552)Aag>Gag	p.K184E		NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	184					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						ACCGGGAGGCAAGGAGCACCT	0.612																																																	0			5											161.0	109.0	127.0					5																	7520992		2203	4300	6503	7573992	SO:0001583	missense	108			AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"""Adenylate cyclases"""	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.550A>G	5.37:g.7520992A>G	ENSP00000342952:p.Lys184Glu		7573992	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	37	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	A	1.318	-0.600199	0.03744	.	.	ENSG00000078295	ENST00000338316;ENST00000541993	T	0.75821	-0.97	5.65	0.2	0.15181	.	0.221927	0.44902	D	0.000403	T	0.51075	0.1653	N	0.20986	0.625	0.29339	N	0.866129	B	0.06786	0.001	B	0.09377	0.004	T	0.36648	-0.9739	10	0.07990	T	0.79	.	7.4678	0.27332	0.5178:0.4078:0.0745:0.0	.	184	Q08462	ADCY2_HUMAN	E	184;35	ENSP00000342952:K184E	ENSP00000342952:K184E	K	+	1	0	ADCY2	7573992	0.764000	0.28473	0.704000	0.30370	0.556000	0.35491	1.342000	0.33919	-0.178000	0.10672	0.528000	0.53228	AAG		0.612	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546	
PRDM9	56979	hgsc.bcm.edu	37	5	23523448	23523448	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:23523448T>C	ENST00000296682.3	+	9	1113	c.931T>C	c.(931-933)Tcc>Ccc	p.S311P		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	311	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						AAAAGATAAATCCTGGGCCAA	0.433										HNSCC(3;0.000094)																																							0			5											131.0	126.0	128.0					5																	23523448		2203	4300	6503	23559205	SO:0001583	missense	56979			AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.931T>C	5.37:g.23523448T>C	ENSP00000296682:p.Ser311Pro		23559205	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	t	8.521	0.868829	0.17322	.	.	ENSG00000164256	ENST00000296682;ENST00000253473	T	0.42131	0.98	3.72	2.39	0.29439	SET domain (2);	0.219316	0.23420	N	0.048377	T	0.36248	0.0960	L	0.48260	1.515	0.09310	N	1	P	0.51791	0.948	P	0.46049	0.502	T	0.24404	-1.0161	10	0.87932	D	0	-13.217	6.4452	0.21871	0.0:0.0:0.252:0.748	.	311	Q9NQV7	PRDM9_HUMAN	P	311;105	ENSP00000296682:S311P	ENSP00000253473:S105P	S	+	1	0	PRDM9	23559205	0.125000	0.22332	0.022000	0.16811	0.058000	0.15608	0.541000	0.23207	1.631000	0.50456	0.483000	0.47432	TCC		0.433	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
C5orf42	65250	hgsc.bcm.edu	37	5	37177738	37177738	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:37177738G>A	ENST00000508244.1	-	29	5978	c.5885C>T	c.(5884-5886)tCg>tTg	p.S1962L	C5orf42_ENST00000425232.2_Missense_Mutation_p.S1962L|C5orf42_ENST00000274258.7_Missense_Mutation_p.S842L			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1962						integral component of membrane (GO:0016021)		p.S842L(1)|p.S1962L(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TTGTTCAGTCGATTTTTCCTC	0.378																																																	2	Substitution - Missense(2)	skin(2)	5											223.0	210.0	214.0					5																	37177738		2203	4300	6503	37213495	SO:0001583	missense	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.5885C>T	5.37:g.37177738G>A	ENSP00000421690:p.Ser1962Leu		37213495	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	G	10.83	1.460971	0.26248	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.23950	1.9;1.9;1.88;1.88	4.9	-1.53	0.08611	.	1.786580	0.03831	N	0.269106	T	0.16642	0.0400	N	0.25647	0.755	0.09310	N	1	B;B	0.14012	0.009;0.009	B;B	0.09377	0.004;0.004	T	0.17868	-1.0355	10	0.30078	T	0.28	.	4.5409	0.12056	0.4453:0.0:0.4079:0.1467	.	1962;842	E9PH94;Q9H799	.;CE042_HUMAN	L	1962;1962;842;1010;842	ENSP00000421690:S1962L;ENSP00000389014:S1962L;ENSP00000274258:S842L;ENSP00000424223:S1010L	ENSP00000274258:S842L	S	-	2	0	C5orf42	37213495	0.001000	0.12720	0.000000	0.03702	0.041000	0.13682	0.142000	0.16096	-0.613000	0.05694	-1.623000	0.00790	TCG		0.378	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
TRAPPC13	80006	hgsc.bcm.edu	37	5	64957892	64957892	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:64957892G>A	ENST00000399438.3	+	11	1258	c.913G>A	c.(913-915)Gat>Aat	p.D305N	TRAPPC13_ENST00000438419.2_Missense_Mutation_p.D305N|TRAPPC13_ENST00000231526.4_Missense_Mutation_p.D299N|TRAPPC13_ENST00000545191.1_Missense_Mutation_p.D306N|TRAPPC13_ENST00000505553.1_Missense_Mutation_p.D299N	NM_001093755.1|NM_024941.3	NP_001087224.1|NP_079217.2	A5PLN9	TPC13_HUMAN	trafficking protein particle complex 13	305																	AGGTTATGGAGATGTTAGGTT	0.378																																																	0			5											179.0	165.0	170.0					5																	64957892		1886	4103	5989	64993648	SO:0001583	missense	80006				CCDS47221.1, CCDS47222.1, CCDS47223.1, CCDS58950.1	5q12.3	2013-01-31	2013-01-24	2013-01-24	ENSG00000113597	ENSG00000113597			25828	protein-coding gene	gene with protein product	"""Trs65-related"""		"""chromosome 5 open reading frame 44"""	C5orf44		12477932	Standard	NM_024941		Approved	FLJ13611, FLJ26957, MGC48585	uc010iwu.1	A5PLN9	OTTHUMG00000163649	ENST00000399438.3:c.913G>A	5.37:g.64957892G>A	ENSP00000382367:p.Asp305Asn		64993648	Q17RZ9|Q49A23|Q4JHG0|Q6MZG4|Q8TCM2|Q9H8I3	Missense_Mutation	SNP	ENST00000399438.3	37	CCDS47222.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.554460	0.86231	.	.	ENSG00000113597	ENST00000399438;ENST00000438419;ENST00000231526;ENST00000505553;ENST00000545191	.	.	.	5.35	4.49	0.54785	.	0.000000	0.85682	D	0.000000	T	0.67776	0.2929	L	0.52823	1.66	0.80722	D	1	D;P;D;D	0.58620	0.983;0.922;0.983;0.972	P;P;P;P	0.59595	0.86;0.781;0.86;0.728	T	0.71563	-0.4555	9	0.72032	D	0.01	-25.4577	14.0851	0.64951	0.072:0.0:0.928:0.0	.	299;299;305;305	A5PLN9-4;A5PLN9-2;A5PLN9-5;A5PLN9	.;.;.;CE044_HUMAN	N	305;305;299;299;306	.	ENSP00000231526:D299N	D	+	1	0	C5orf44	64993648	1.000000	0.71417	0.999000	0.59377	0.945000	0.59286	9.156000	0.94705	1.493000	0.48517	0.557000	0.71058	GAT		0.378	TRAPPC13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370113.1	NM_024941	
GPR98	84059	hgsc.bcm.edu	37	5	90074423	90074423	+	Silent	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:90074423G>A	ENST00000405460.2	+	63	12942	c.12846G>A	c.(12844-12846)caG>caA	p.Q4282Q	GPR98_ENST00000425867.2_5'Flank	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4282	Calx-beta 29. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CAGAAGCACAGAGGGTATAGT	0.383																																																	0			5											45.0	43.0	43.0					5																	90074423		1918	4127	6045	90110179	SO:0001819	synonymous_variant	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.12846G>A	5.37:g.90074423G>A			90110179	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1																																																																																				0.383	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
SPATA9	83890	hgsc.bcm.edu	37	5	94994411	94994411	+	Silent	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:94994411C>T	ENST00000274432.8	-	5	822	c.681G>A	c.(679-681)aaG>aaA	p.K227K	RFESD_ENST00000508206.1_Intron|SPATA9_ENST00000477047.2_Intron	NM_031952.3	NP_114158.2	Q9BWV2	SPAT9_HUMAN	spermatogenesis associated 9	227					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)	7		all_cancers(142;1.28e-06)|all_epithelial(76;1.55e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.91e-16)		TAGCAAGAAGCTTGGGGTAAT	0.408																																																	0			5											93.0	93.0	93.0					5																	94994411		2203	4299	6502	95020167	SO:0001819	synonymous_variant	83890			AK093225	CCDS4076.1	5q15	2008-02-05			ENSG00000145757	ENSG00000145757			22988	protein-coding gene	gene with protein product		608039				12493713	Standard	NM_031952		Approved	NYD-SP16, FLJ35906	uc003klj.1	Q9BWV2	OTTHUMG00000121169	ENST00000274432.8:c.681G>A	5.37:g.94994411C>T			95020167	A8K8H3|Q4G122|Q86X33|Q8NA28	Silent	SNP	ENST00000274432.8	37	CCDS4076.1																																																																																				0.408	SPATA9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304036.1	NM_031952	
APC	324	hgsc.bcm.edu	37	5	112173346	112173346	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:112173346G>A	ENST00000457016.1	+	16	2435	c.2055G>A	c.(2053-2055)tgG>tgA	p.W685*	APC_ENST00000508376.2_Nonsense_Mutation_p.W685*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.W685*			P25054	APC_HUMAN	adenomatous polyposis coli	685	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.W685*(2)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAACTTTGTGGAATCTCTCAG	0.383		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	3	Substitution - Nonsense(2)|Unknown(1)	large_intestine(1)|lung(1)|skin(1)	5	GRCh37	CM931177	APC	M							95.0	96.0	95.0					5																	112173346		2202	4300	6502	112201245	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2055G>A	5.37:g.112173346G>A	ENSP00000413133:p.Trp685*		112201245	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	36	5.886725	0.97068	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.3726	20.4777	0.99188	0.0:0.0:1.0:0.0	.	.	.	.	X	685;667;685;685;685	.	ENSP00000257430:W685X	W	+	3	0	APC	112201245	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.840000	0.97914	0.655000	0.94253	TGG		0.383	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	hgsc.bcm.edu	37	5	112175257	112175257	+	Silent	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:112175257A>G	ENST00000457016.1	+	16	4346	c.3966A>G	c.(3964-3966)gaA>gaG	p.E1322E	APC_ENST00000508376.2_Silent_p.E1322E|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.E1322E			P25054	APC_HUMAN	adenomatous polyposis coli	1322	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.V1320fs*8(1)|p.K1192fs*3(1)|p.?(1)|p.E1322fs*8(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTGTGAGCGAAGTTCCAGCAG	0.438		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	4	Deletion - Frameshift(3)|Unknown(1)	large_intestine(2)|soft_tissue(1)|skin(1)	5	GRCh37	CI931064	APC	I							61.0	63.0	62.0					5																	112175257		2202	4300	6502	112203156	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3966A>G	5.37:g.112175257A>G			112203156	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.438	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	hgsc.bcm.edu	37	5	112175456	112175456	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:112175456T>C	ENST00000457016.1	+	16	4545	c.4165T>C	c.(4165-4167)Tct>Cct	p.S1389P	APC_ENST00000508376.2_Missense_Mutation_p.S1389P|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.S1389P			P25054	APC_HUMAN	adenomatous polyposis coli	1389	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1389fs*5(3)|p.Y1376fs*41(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGATGTACTTCTGTCAGTTC	0.473		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	6	Deletion - Frameshift(5)|Unknown(1)	large_intestine(4)|soft_tissue(1)|skin(1)	5											106.0	100.0	102.0					5																	112175456		2202	4300	6502	112203355	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4165T>C	5.37:g.112175456T>C	ENSP00000413133:p.Ser1389Pro		112203355	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.065285	0.76187	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.94537	-3.45;-3.45;-3.45	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.96460	0.8845	L	0.58810	1.83	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.96010	0.9001	9	.	.	.	-15.765	16.4957	0.84242	0.0:0.0:0.0:1.0	.	1391;1389	Q4LE70;P25054	.;APC_HUMAN	P	1389	ENSP00000413133:S1389P;ENSP00000257430:S1389P;ENSP00000427089:S1389P	.	S	+	1	0	APC	112203355	1.000000	0.71417	0.991000	0.47740	0.920000	0.55202	7.698000	0.84413	2.371000	0.80710	0.533000	0.62120	TCT		0.473	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
TRIM36	55521	hgsc.bcm.edu	37	5	114469752	114469752	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:114469752T>C	ENST00000282369.3	-	8	1460	c.1339A>G	c.(1339-1341)Agc>Ggc	p.S447G	TRIM36_ENST00000513154.1_Missense_Mutation_p.S435G|TRIM36_ENST00000514154.1_Missense_Mutation_p.S292G	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	447	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				acrosome reaction (GO:0007340)|regulation of cell cycle (GO:0051726)	acrosomal vesicle (GO:0001669)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S447C(1)		breast(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	37		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		AGAACATAGCTATCAGCTTTA	0.358																																																	1	Substitution - Missense(1)	lung(1)	5											121.0	112.0	115.0					5																	114469752		2202	4300	6502	114497651	SO:0001583	missense	55521			AJ272269	CCDS4115.1, CCDS34211.1, CCDS34212.1, CCDS75287.1	5q22	2013-02-11	2011-01-25		ENSG00000152503	ENSG00000152503		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	16280	protein-coding gene	gene with protein product	"""zinc-binding protein Rbcc728"", ""tripartite motif protein 36"", ""RING finger protein 98"""	609317	"""tripartite motif-containing 36"""			11331580	Standard	XM_005272031		Approved	RBCC728, RNF98, HAPRIN	uc003kqs.3	Q9NQ86	OTTHUMG00000128892	ENST00000282369.3:c.1339A>G	5.37:g.114469752T>C	ENSP00000282369:p.Ser447Gly		114497651	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Missense_Mutation	SNP	ENST00000282369.3	37	CCDS4115.1	.	.	.	.	.	.	.	.	.	.	T	9.403	1.078465	0.20227	.	.	ENSG00000152503	ENST00000282369;ENST00000513154;ENST00000514154	T;T;T	0.52526	0.66;0.66;0.66	5.63	4.48	0.54585	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.472746	0.24681	N	0.036478	T	0.30355	0.0762	N	0.22421	0.69	0.80722	D	1	B;B	0.14012	0.003;0.009	B;B	0.17979	0.01;0.02	T	0.08597	-1.0714	10	0.10636	T	0.68	.	11.0049	0.47629	0.0:0.0724:0.0:0.9276	.	435;447	E9PFI8;Q9NQ86	.;TRI36_HUMAN	G	447;435;292	ENSP00000282369:S447G;ENSP00000423934:S435G;ENSP00000424259:S292G	ENSP00000282369:S447G	S	-	1	0	TRIM36	114497651	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	2.842000	0.48230	2.145000	0.66743	0.533000	0.62120	AGC		0.358	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700	
PCDHA9	9752	hgsc.bcm.edu	37	5	140229951	140229951	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:140229951T>C	ENST00000532602.1	+	1	2904	c.1871T>C	c.(1870-1872)gTg>gCg	p.V624A	PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.V624A|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	624	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGTTCCGCGTGGGGCTGTAC	0.667																																					Melanoma(55;1800 1972 14909)												0			5											69.0	73.0	72.0					5																	140229951		2197	4274	6471	140210135	SO:0001583	missense	9752			AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"""Cadherins / Protocadherins : Clustered"""	8675	other	complex locus constituent	"""KIAA0345-like 5"""	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1871T>C	5.37:g.140229951T>C	ENSP00000436042:p.Val624Ala		140210135	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	T	15.47	2.842564	0.51057	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.59772	0.24;0.24	4.05	4.05	0.47172	Cadherin (4);Cadherin-like (1);	0.382752	0.15065	U	0.282541	D	0.83608	0.5291	H	0.97415	4	0.23872	N	0.996605	D;D	0.67145	0.985;0.996	D;D	0.76071	0.928;0.987	T	0.76940	-0.2773	10	0.87932	D	0	.	12.9417	0.58348	0.0:0.0:0.0:1.0	.	624;624	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	A	624	ENSP00000436042:V624A;ENSP00000367362:V624A	ENSP00000367362:V624A	V	+	2	0	PCDHA9	140210135	0.996000	0.38824	1.000000	0.80357	0.186000	0.23388	1.923000	0.40055	1.579000	0.49836	0.260000	0.18958	GTG		0.667	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857	
PCDHA12	56137	hgsc.bcm.edu	37	5	140256623	140256623	+	Silent	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:140256623G>A	ENST00000398631.2	+	1	1566	c.1566G>A	c.(1564-1566)ccG>ccA	p.P522P	PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	522	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCTGCAGCCGCTAGACCACG	0.692																																					Pancreas(113;759 1672 13322 24104 50104)												0			5											78.0	85.0	82.0					5																	140256623		2203	4298	6501	140236807	SO:0001819	synonymous_variant	56137			AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"""Cadherins / Protocadherins : Clustered"""	8666	other	complex locus constituent	"""KIAA0345-like 2"""	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1566G>A	5.37:g.140256623G>A			140236807	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	37	CCDS47285.1																																																																																				0.692	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903	
PCDHB5	26167	hgsc.bcm.edu	37	5	140515027	140515027	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:140515027C>T	ENST00000231134.5	+	1	228	c.11C>T	c.(10-12)gCg>gTg	p.A4V		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	4					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ATGGAGACTGCGCTAGCAAAA	0.458																																																	0			5											88.0	78.0	81.0					5																	140515027		2203	4300	6503	140495211	SO:0001583	missense	26167			AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"""Cadherins / Protocadherins : Clustered"""	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.11C>T	5.37:g.140515027C>T	ENSP00000231134:p.Ala4Val		140495211	Q549F4|Q9UFU9	Missense_Mutation	SNP	ENST00000231134.5	37	CCDS4247.1	.	.	.	.	.	.	.	.	.	.	C	19.06	3.753099	0.69648	.	.	ENSG00000113209	ENST00000231134	T	0.51071	0.72	5.38	4.46	0.54185	.	.	.	.	.	T	0.45418	0.1341	L	0.57536	1.79	0.09310	N	1	B	0.16166	0.016	B	0.14578	0.011	T	0.22556	-1.0213	9	0.30078	T	0.28	.	14.0354	0.64642	0.212:0.788:0.0:0.0	.	4	Q9Y5E4	PCDB5_HUMAN	V	4	ENSP00000231134:A4V	ENSP00000231134:A4V	A	+	2	0	PCDHB5	140495211	0.000000	0.05858	0.557000	0.28306	0.970000	0.65996	0.631000	0.24568	2.687000	0.91594	0.561000	0.74099	GCG		0.458	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669	
PCDHB7	56129	hgsc.bcm.edu	37	5	140553439	140553439	+	Silent	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:140553439C>T	ENST00000231137.3	+	1	1197	c.1023C>T	c.(1021-1023)aaC>aaT	p.N341N		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	341	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAGATATAAACGATAATCGAC	0.443																																																	0			5											46.0	47.0	46.0					5																	140553439		2203	4300	6503	140533623	SO:0001819	synonymous_variant	56129			AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.1023C>T	5.37:g.140553439C>T			140533623	A1L3Y8	Silent	SNP	ENST00000231137.3	37	CCDS4249.1																																																																																				0.443	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
PCDHGC5	56097	hgsc.bcm.edu	37	5	140870546	140870546	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:140870546C>T	ENST00000252087.1	+	1	1739	c.1739C>T	c.(1738-1740)cCt>cTt	p.P580L	PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGC4_ENST00000306593.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA7_ENST00000518325.1_Intron	NM_018929.2|NM_032403.2|NM_032407.1	NP_061752.1|NP_115779.1|NP_115783.1	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5	580	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGCGTCTCCCTCGCTCTGCT	0.587																																																	0			5											61.0	55.0	57.0					5																	140870546		2203	4300	6503	140850730	SO:0001583	missense	56097			AF152526	CCDS4263.1, CCDS75350.1	5q31	2010-01-26			ENSG00000240764	ENSG00000240764		"""Cadherins / Protocadherins : Clustered"""	8718	other	protocadherin		606306				10380929	Standard	NM_018929		Approved	PCDH-GAMMA-C5	uc003lla.2	Q9Y5F6	OTTHUMG00000129624	ENST00000252087.1:c.1739C>T	5.37:g.140870546C>T	ENSP00000252087:p.Pro580Leu		140850730	Q9Y5C2	Missense_Mutation	SNP	ENST00000252087.1	37	CCDS4263.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.465826	0.43839	.	.	ENSG00000240764	ENST00000252087	T	0.21031	2.03	5.45	4.55	0.56014	Cadherin (2);Cadherin-like (1);	0.363922	0.23902	N	0.043431	T	0.40670	0.1126	M	0.62154	1.92	0.54753	D	0.999986	D;P	0.76494	0.999;0.825	D;P	0.70935	0.971;0.492	T	0.10405	-1.0631	10	0.66056	D	0.02	.	11.6309	0.51173	0.0:0.7849:0.1385:0.0766	.	580;580	Q9Y5F6-2;Q9Y5F6	.;PCDGM_HUMAN	L	580	ENSP00000252087:P580L	ENSP00000252087:P580L	P	+	2	0	PCDHGC5	140850730	0.676000	0.27567	1.000000	0.80357	0.999000	0.98932	0.973000	0.29422	2.833000	0.97629	0.655000	0.94253	CCT		0.587	PCDHGC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251819.1	NM_018929	
PDE6A	5145	hgsc.bcm.edu	37	5	149324228	149324228	+	Missense_Mutation	SNP	C	C	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:149324228C>A	ENST00000255266.5	-	1	128	c.9G>T	c.(7-9)gaG>gaT	p.E3D		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	3					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	CTGCTGTCACCTCGCCCATGG	0.552																																																	0			5											32.0	28.0	29.0					5																	149324228		2203	4300	6503	149304421	SO:0001583	missense	5145				CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.9G>T	5.37:g.149324228C>A	ENSP00000255266:p.Glu3Asp		149304421	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	37	CCDS4299.1	.	.	.	.	.	.	.	.	.	.	C	11.32	1.603535	0.28534	.	.	ENSG00000132915	ENST00000255266	T	0.63744	-0.06	5.79	-0.951	0.10369	.	0.200405	0.43747	D	0.000527	T	0.48333	0.1494	L	0.46157	1.445	0.30985	N	0.722104	B	0.11235	0.004	B	0.11329	0.006	T	0.42498	-0.9448	10	0.33940	T	0.23	.	8.7182	0.34425	0.0:0.3758:0.0:0.6242	.	3	P16499	PDE6A_HUMAN	D	3	ENSP00000255266:E3D	ENSP00000255266:E3D	E	-	3	2	PDE6A	149304421	0.194000	0.23325	0.972000	0.41901	0.524000	0.34500	-0.600000	0.05693	-0.090000	0.12462	-0.254000	0.11334	GAG		0.552	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
KCNIP1	30820	hgsc.bcm.edu	37	5	170162792	170162792	+	Silent	SNP	G	G	A			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:170162792G>A	ENST00000411494.1	+	9	666	c.666G>A	c.(664-666)ctG>ctA	p.L222L	KCNIP1_ENST00000328939.4_Silent_p.L211L|KCNIP1_ENST00000434108.1_Silent_p.L236L|KCNIP1_ENST00000390656.4_Silent_p.L211L|KCNIP1_ENST00000520740.1_Silent_p.L183L|KCNIP1_ENST00000377360.4_Silent_p.L220L			Q9NZI2	KCIP1_HUMAN	Kv channel interacting protein 1	222	Interaction with KCND2. {ECO:0000250}.				detection of calcium ion (GO:0005513)|positive regulation of action potential (GO:0045760)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|potassium channel complex (GO:0034705)	calcium ion binding (GO:0005509)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|voltage-gated ion channel activity (GO:0005244)			autonomic_ganglia(1)|large_intestine(7)|lung(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	18	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTCTCCAGCTGTTTCAAAATG	0.473																																																	0			5											135.0	123.0	127.0					5																	170162792		2203	4300	6503	170095370	SO:0001819	synonymous_variant	30820			AF199597	CCDS34285.1, CCDS34286.1, CCDS4374.1, CCDS64312.1, CCDS64313.1	5q35	2013-01-10			ENSG00000182132	ENSG00000182132		"""EF-hand domain containing"""	15521	protein-coding gene	gene with protein product		604660				10676964	Standard	NM_001278339		Approved	KCHIP1	uc003map.3	Q9NZI2	OTTHUMG00000130442	ENST00000411494.1:c.666G>A	5.37:g.170162792G>A			170095370	B7Z7B4|Q3YAD0|Q3YAD1|Q3YAD2|Q3YAD3|Q5U822	Silent	SNP	ENST00000411494.1	37	CCDS34286.1																																																																																				0.473	KCNIP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000371760.1		
HK3	3101	hgsc.bcm.edu	37	5	176314614	176314614	+	Missense_Mutation	SNP	G	G	A	rs376532514		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr5:176314614G>A	ENST00000292432.5	-	11	1529	c.1438C>T	c.(1438-1440)Cgg>Tgg	p.R480W		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	480	Hexokinase type-1 2.|Regulatory.		R -> W (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)	p.R480W(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGCAGGCGCCGGTGGGCAGCC	0.662																																																	1	Substitution - Missense(1)	large_intestine(1)	5						G	TRP/ARG	0,4406		0,0,2203	32.0	32.0	32.0		1438	1.4	1.0	5		32	1,8599	1.2+/-3.3	0,1,4299	no	missense	HK3	NM_002115.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	480/924	176314614	1,13005	2203	4300	6503	176247220	SO:0001583	missense	84376				CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.1438C>T	5.37:g.176314614G>A	ENSP00000292432:p.Arg480Trp		176247220	Q8N1E7	Missense_Mutation	SNP	ENST00000292432.5	37	CCDS4407.1	.	.	.	.	.	.	.	.	.	.	G	12.41	1.929608	0.34096	0.0	1.16E-4	ENSG00000160883	ENST00000292432	D	0.98296	-4.85	4.43	1.43	0.22495	Hexokinase, N-terminal (1);	0.319071	0.22897	N	0.054307	D	0.98005	0.9343	M	0.78801	2.425	0.33245	D	0.5578	D	0.64830	0.994	P	0.58820	0.846	D	0.97198	0.9862	10	0.59425	D	0.04	-16.9109	6.465	0.21977	0.0881:0.0:0.5593:0.3525	.	480	P52790	HXK3_HUMAN	W	480	ENSP00000292432:R480W	ENSP00000292432:R480W	R	-	1	2	HK3	176247220	0.997000	0.39634	0.966000	0.40874	0.008000	0.06430	2.526000	0.45607	-0.045000	0.13468	-1.334000	0.01262	CGG		0.662	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		
TP53	7157	hgsc.bcm.edu	37	17	7579591	7579591	+	Splice_Site	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:7579591C>T	ENST00000269305.4	-	4	286		c.e4-1		TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000413465.2_Splice_Site|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Splice_Site	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(8)|p.0?(8)|p.L35fs*10(3)|p.S33fs*10(1)|p.P13fs*18(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCAAGGGGGACTGTAGATGGG	0.592		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	21	Unknown(11)|Whole gene deletion(8)|Insertion - Frameshift(1)|Deletion - Frameshift(1)	bone(4)|large_intestine(3)|central_nervous_system(3)|lung(3)|pancreas(3)|upper_aerodigestive_tract(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)	17	GRCh37	CS971912	TP53	S							141.0	137.0	138.0					17																	7579591		2203	4300	6503	7520316	SO:0001630	splice_region_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.97-1G>A	17.37:g.7579591C>T			7520316	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	6.702	0.498192	0.12762	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	.	.	.	2.49	2.49	0.30216	.	.	.	.	.	.	.	.	.	.	.	0.40380	D	0.979434	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6143	0.33822	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7520316	0.879000	0.30193	0.021000	0.16686	0.027000	0.11550	1.937000	0.40193	1.730000	0.51580	0.561000	0.74099	.		0.592	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron
SLC12A6	9990	hgsc.bcm.edu	37	15	34527516	34527516	+	Splice_Site	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr15:34527516C>T	ENST00000354181.3	-	25	3720		c.e25-1		SLC12A6_ENST00000558667.1_Splice_Site|SLC12A6_ENST00000458406.2_Splice_Site|SLC12A6_ENST00000560611.1_Splice_Site|SLC12A6_ENST00000397702.2_Splice_Site|SLC12A6_ENST00000560164.1_Splice_Site|SLC12A6_ENST00000397707.2_Splice_Site|SLC12A6_ENST00000451844.2_Splice_Site|SLC12A6_ENST00000558589.1_Splice_Site|SLC12A6_ENST00000290209.5_Splice_Site			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6						angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	GGACTGGTCCCTGAGTGGGGA	0.403																																																	0			15											77.0	70.0	72.0					15																	34527516		2201	4298	6499	32314808	SO:0001630	splice_region_variant	9990			AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"""Solute carriers"""	10914	protein-coding gene	gene with protein product		604878	"""agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"""	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.3228-1G>A	15.37:g.34527516C>T			32314808	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Splice_Site	SNP	ENST00000354181.3	37	CCDS58352.1	.	.	.	.	.	.	.	.	.	.	C	16.07	3.018194	0.54576	.	.	ENSG00000140199	ENST00000290209;ENST00000397707;ENST00000354181;ENST00000397702;ENST00000458406;ENST00000451844	.	.	.	5.04	5.04	0.67666	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.3256	0.87246	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC12A6	32314808	1.000000	0.71417	0.999000	0.59377	0.382000	0.30200	7.307000	0.78920	2.617000	0.88574	0.561000	0.74099	.		0.403	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135	Intron
ZFX	7543	hgsc.bcm.edu	37	X	24225594	24225594	+	Splice_Site	SNP	T	T	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chrX:24225594T>G	ENST00000379177.1	+	7	1223		c.e7+2		ZFX_ENST00000338565.3_Intron|ZFX_ENST00000459724.1_Splice_Site|ZFX_ENST00000540034.1_Splice_Site|ZFX_ENST00000304543.5_Splice_Site|ZFX_ENST00000539115.1_Splice_Site|ZFX_ENST00000379188.3_Splice_Site	NM_001178085.1|NM_003410.3	NP_001171556.1|NP_003401.2	P17010	ZFX_HUMAN	zinc finger protein, X-linked						death (GO:0016265)|fertilization (GO:0009566)|homeostasis of number of cells (GO:0048872)|multicellular organism growth (GO:0035264)|oocyte development (GO:0048599)|ovarian follicle development (GO:0001541)|parental behavior (GO:0060746)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)			cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(2)|lung(4)|ovary(2)|prostate(1)	24						ATGACTTAGGTAAGAAGAAGT	0.393																																					Esophageal Squamous(20;306 562 7346 32868 37983)												0			X											129.0	116.0	120.0					X																	24225594		2203	4300	6503	24135515	SO:0001630	splice_region_variant	7543				CCDS14211.1, CCDS55390.1	Xp22.1-p21.3	2013-01-08			ENSG00000005889	ENSG00000005889		"""Zinc fingers, C2H2-type"""	12869	protein-coding gene	gene with protein product		314980					Standard	NM_003410		Approved	ZNF926	uc022bua.1	P17010	OTTHUMG00000021264	ENST00000379177.1:c.796+2T>G	X.37:g.24225594T>G			24135515	B9EG97|O43668|Q8WYJ8	Splice_Site	SNP	ENST00000379177.1	37	CCDS14211.1	.	.	.	.	.	.	.	.	.	.	T	16.02	3.004629	0.54254	.	.	ENSG00000005889	ENST00000539115;ENST00000379188;ENST00000535562;ENST00000379177;ENST00000304543;ENST00000540034;ENST00000545937	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4962	0.67688	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZFX	24135515	1.000000	0.71417	0.997000	0.53966	0.818000	0.46254	7.655000	0.83696	1.871000	0.54225	0.481000	0.45027	.		0.393	ZFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056084.1	NM_003410	Intron
TNIP2	79155	hgsc.bcm.edu	37	4	2744248	2744248	+	Splice_Site	SNP	C	C	T			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:2744248C>T	ENST00000315423.7	-	6	1113		c.e6-1		TNIP2_ENST00000505186.1_Splice_Site|TNIP2_ENST00000510267.1_Splice_Site|TNIP2_ENST00000503235.1_Splice_Site	NM_024309.3	NP_077285.3			TNFAIP3 interacting protein 2											breast(2)|central_nervous_system(1)|large_intestine(4)|lung(6)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CTCGAGAATCCTGGAGAAAAG	0.572																																																	0			4											30.0	32.0	32.0					4																	2744248		2203	4300	6503	2714046	SO:0001630	splice_region_variant	79155			BC002740	CCDS3362.1, CCDS54714.1, CCDS75093.1	4p16.3	2008-08-01			ENSG00000168884	ENSG00000168884			19118	protein-coding gene	gene with protein product		610669				11390377, 12933576	Standard	NM_024309		Approved	ABIN-2, MGC4289, KLIP, FLIP1	uc003gfg.2	Q8NFZ5	OTTHUMG00000090267	ENST00000315423.7:c.1027-1G>A	4.37:g.2744248C>T			2714046		Splice_Site	SNP	ENST00000315423.7	37	CCDS3362.1	.	.	.	.	.	.	.	.	.	.	C	11.59	1.683216	0.29872	.	.	ENSG00000168884	ENST00000510267;ENST00000315423;ENST00000503235	.	.	.	4.02	4.02	0.46733	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.219	0.73296	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TNIP2	2714046	1.000000	0.71417	0.994000	0.49952	0.218000	0.24690	4.261000	0.58841	2.252000	0.74401	0.561000	0.74099	.		0.572	TNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206589.5	NM_024309	Intron
PRKG1	5592	hgsc.bcm.edu	37	10	53822295	53822295	+	Splice_Site	SNP	A	A	G			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:53822295A>G	ENST00000401604.2	+	7	989		c.e7-1		PRKG1_ENST00000373975.2_Splice_Site|PRKG1_ENST00000373985.1_Splice_Site|PRKG1_ENST00000373980.4_Splice_Site			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I						actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)	p.?(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		TTCTCTTTGCAGGTAAATGTC	0.393																																																	1	Unknown(1)	ovary(1)	10											63.0	61.0	62.0					10																	53822295		2203	4300	6503	53492301	SO:0001630	splice_region_variant	5592				CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.796-1A>G	10.37:g.53822295A>G			53492301	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Splice_Site	SNP	ENST00000401604.2	37	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	A	18.90	3.722065	0.68959	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000373976	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0391	0.64663	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PRKG1	53492301	1.000000	0.71417	0.932000	0.37286	0.784000	0.44337	8.793000	0.91862	2.202000	0.70862	0.533000	0.62120	.		0.393	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Intron
LCE4A	199834	hgsc.bcm.edu	37	1	152681680	152681681	+	In_Frame_Ins	INS	-	-	AGCTCTGGGGGCTGCTGT	rs6143428|rs11269814|rs200890315|rs33921874	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:152681680_152681681insAGCTCTGGGGGCTGCTGT	ENST00000368777.1	+	2	385_386	c.129_130insAGCTCTGGGGGCTGCTGT	c.(130-132)agc>AGCTCTGGGGGCTGCTGTagc	p.44_44S>SSGGCCS	LCE4A_ENST00000335535.3_In_Frame_Ins_p.44_44S>SSGGCCS			Q5TA78	LCE4A_HUMAN	late cornified envelope 4A	44	Cys-rich.				keratinization (GO:0031424)					endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.116)			GCTGTGGCTCCAGCTCTGGGGG	0.599														4009	0.800519	0.9758	0.853	5008	,	,		18534	0.6855		0.7177	False		,,,				2504	0.7301																0			1																																								150948305	SO:0001652	inframe_insertion	199834			BI670517	CCDS1022.1	1q22	2008-02-05	2004-10-11	2004-10-15	ENSG00000187170	ENSG00000187170		"""Late cornified envelopes"""	16613	protein-coding gene	gene with protein product		612618	"""small proline rich-like (epidermal differentiation complex) 4A"""	SPRL4A		11698679	Standard	NM_178356		Approved	LEP8	uc001fak.2	Q5TA78	OTTHUMG00000014394	Exception_encountered	1.37:g.152681680_152681681insAGCTCTGGGGGCTGCTGT	Exception_encountered		150948304	Q14D97	In_Frame_Ins	INS	ENST00000368777.1	37	CCDS1022.1																																																																																				0.599	LCE4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040048.1	NM_178356	
PRG4	10216	hgsc.bcm.edu	37	1	186276284	186276286	+	In_Frame_Del	DEL	CTC	CTC	-	rs200031345|rs145095882|rs143141440	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	CTC	CTC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:186276284_186276286delCTC	ENST00000445192.2	+	7	1478_1480	c.1433_1435delCTC	c.(1432-1437)actccc>acc	p.P479del	PRG4_ENST00000367483.4_In_Frame_Del_p.P438del|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367485.4_In_Frame_Del_p.P386del|PRG4_ENST00000367486.3_In_Frame_Del_p.P436del	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	479	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.P479delP(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						GCACCCACCACTCCCAAAGAGCC	0.65																																																	1	Deletion - In frame(1)	large_intestine(1)	1							,,,	348,3912		14,320,1796					,,,	-1.4	0.0			89	1023,7215		71,881,3167	no	coding,coding,coding,coding	PRG4	NM_005807.3,NM_001127710.1,NM_001127709.1,NM_001127708.1	,,,	85,1201,4963	A1A1,A1R,RR		12.4181,8.169,10.9698	,,,	,,,		1371,11127				184542909	SO:0001651	inframe_deletion	23572			U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1433_1435delCTC	1.37:g.186276284_186276286delCTC	ENSP00000399679:p.Pro479del		184542907	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	In_Frame_Del	DEL	ENST00000445192.2	37	CCDS1369.1																																																																																				0.650	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
PRKRA	8575	hgsc.bcm.edu	37	2	179315735	179315736	+	Frame_Shift_Del	DEL	GC	GC	-	rs141354030|rs79769305	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	GC	GC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:179315735_179315736delGC	ENST00000325748.4	-	1	222_223	c.22_23delGC	c.(22-24)gccfs	p.A8fs	PRKRA_ENST00000487082.1_5'Flank|DFNB59_ENST00000375129.4_5'Flank|PRKRA_ENST00000432031.2_5'Flank|PRKRA_ENST00000438687.3_5'UTR|DFNB59_ENST00000409117.3_5'Flank|PRKRA_ENST00000470200.1_5'UTR	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator	8	Sufficient for self-association and interaction with TARBP2.				cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			CGGGGCCTCGGCGCGGTGCCTG	0.757														1193	0.238219	0.1649	0.3545	5008	,	,		12129	0.123		0.339	False		,,,				2504	0.2699				Melanoma(200;68 3001 23825 48764)												0			2								658,2174		225,208,983						-1.9	0.8		dbSNP_134	7	2206,4138		751,704,1717	no	frameshift	PRKRA	NM_003690.4		976,912,2700	A1A1,A1R,RR		34.773,23.2345,31.2119				2864,6312				179023982	SO:0001589	frameshift_variant	8575			AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"""protein activator of the interferon-induced protein kinase"""	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.22_23delGC	2.37:g.179315737_179315738delGC	ENSP00000318176:p.Ala8fs		179023981	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Frame_Shift_Del	DEL	ENST00000325748.4	37	CCDS2279.1																																																																																				0.757	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690	
MUC4	4585	hgsc.bcm.edu	37	3	195508202	195508249	+	In_Frame_Del	DEL	CTGAGGAAGGGCTAGTGACAGGAAGAGGCATGGTGTCACCTGTGGATA	CTGAGGAAGGGCTAGTGACAGGAAGAGGCATGGTGTCACCTGTGGATA	-	rs558318316|rs199592227|rs566665732|rs144373027|rs138141889|rs542067128|rs144420167|rs576510701|rs533775458|rs200984123|rs537584428|rs201826718|rs536470139|rs574664481|rs201846606	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	CTGAGGAAGGGCTAGTGACAGGAAGAGGCATGGTGTCACCTGTGGATA	CTGAGGAAGGGCTAGTGACAGGAAGAGGCATGGTGTCACCTGTGGATA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:195508202_195508249delCTGAGGAAGGGCTAGTGACAGGAAGAGGCATGGTGTCACCTGTGGATA	ENST00000463781.3	-	2	10661_10708	c.10202_10249delTATCCACAGGTGACACCATGCCTCTTCCTGTCACTAGCCCTTCCTCAG	c.(10201-10251)gtatccacaggtgacaccatgcctcttcctgtcactagcccttcctcagca>gca	p.VSTGDTMPLPVTSPSS3401del	MUC4_ENST00000475231.1_In_Frame_Del_p.VSTGDTMPLPVTSPSS3401del|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V3401A(3)|p.P3408R(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CCTGTGGATGCTGAGGAAGGGCTAGTGACAGGAAGAGGCATGGTGTCACCTGTGGATACTGAGGAAGT	0.585																																																	4	Substitution - Missense(4)	stomach(2)|kidney(1)|endometrium(1)	3							,,	191,3561		48,95,1733					,,	-0.4	0.0			12	700,6748		140,420,3164	no	intron,coding,intron	MUC4	NM_138297.4,NM_018406.6,NM_004532.5	,,	188,515,4897	A1A1,A1R,RR		9.3985,5.0906,7.9554	,,	,,		891,10309				196993028	SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10202_10249delTATCCACAGGTGACACCATGCCTCTTCCTGTCACTAGCCCTTCCTCAG	3.37:g.195508202_195508249delCTGAGGAAGGGCTAGTGACAGGAAGAGGCATGGTGTCACCTGTGGATA	ENSP00000417498:p.Val3401_Ser3416del		196992981	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				0.585	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195515367	195515414	+	In_Frame_Del	DEL	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	-	rs369312980|rs547775645|rs201510137|rs200193644|rs531942134|rs13060431|rs200400545|rs71180964|rs199583597|rs55868431|rs55803325|rs550428312|rs199702053|rs13065584	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:195515367_195515414delGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	ENST00000463781.3	-	2	3496_3543	c.3037_3084delAGCCCTTCCTCAGTATCCACAGGTCACACCACCCCTCTTCCTGTCACC	c.(3037-3084)agcccttcctcagtatccacaggtcacaccacccctcttcctgtcaccdel	p.SPSSVSTGHTTPLPVT1013del	MUC4_ENST00000475231.1_In_Frame_Del_p.SPSSVSTGHTTPLPVT1013del|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	448	Repeat.|Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1013_T1028delSPSSVSTGHTTPLPVT(4)|p.S1013G(2)|p.T1022A(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGTGTCGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCTGGTGACAGGA	0.573																																																	8	Substitution - Missense(4)|Deletion - In frame(4)	stomach(6)|prostate(2)	3																																								196999809	SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3037_3084delAGCCCTTCCTCAGTATCCACAGGTCACACCACCCCTCTTCCTGTCACC	3.37:g.195515367_195515414delGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	ENSP00000417498:p.Ser1013_Thr1028del		196999762	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				0.573	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388504	1388505	+	Frame_Shift_Del	DEL	CG	CG	-	rs568118449|rs528384190|rs115485610	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	CG	CG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:1388504_1388505delCG	ENST00000324803.4	+	1	3165_3166	c.205_206delCG	c.(205-207)cgtfs	p.R69fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	69					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			TGCTCACACACGTGTCCATGTG	0.629														54	0.0107827	0.0174	0.0043	5008	,	,		20699	0.002		0.0169	False		,,,				2504	0.0092																0			4																																								1378505	SO:0001589	frameshift_variant	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.205_206delCG	4.37:g.1388504_1388505delCG	ENSP00000323978:p.Arg69fs		1378504	Q8NB03	Frame_Shift_Del	DEL	ENST00000324803.4	37	CCDS3349.1																																																																																				0.629	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
C6orf132	647024	hgsc.bcm.edu	37	6	42075105	42075131	+	In_Frame_Del	DEL	GGTGGGGGTTCCAGCAGCAGGGGAGGT	GGTGGGGGTTCCAGCAGCAGGGGAGGT	-	rs553334748|rs539692316	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	GGTGGGGGTTCCAGCAGCAGGGGAGGT	GGTGGGGGTTCCAGCAGCAGGGGAGGT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr6:42075105_42075131delGGTGGGGGTTCCAGCAGCAGGGGAGGT	ENST00000341865.4	-	4	518_544	c.519_545delACCTCCCCTGCTGCTGGAACCCCCACC	c.(517-546)ccacctcccctgctgctggaacccccaccc>ccc	p.173_182PPPLLLEPPP>P		NM_001164446.1	NP_001157918.1	Q5T0Z8	CF132_HUMAN	chromosome 6 open reading frame 132	173	Pro-rich.									breast(1)	1						gctgggcgggggtgggggttccagcagcaggggaggtggtgggggtg	0.665																																																	0			6								8,1312		4,0,656						1.1	0.5			2	76,2832		27,22,1405	no	coding	C6orf132	NM_001164446.1		31,22,2061	A1A1,A1R,RR		2.6135,0.6061,1.9868				84,4144				42183109	SO:0001651	inframe_deletion	647024				CCDS47428.1	6p21.1	2012-02-06			ENSG00000188112	ENSG00000188112			21288	protein-coding gene	gene with protein product							Standard	NM_001164446		Approved	bA7K24.2	uc003orw.2	Q5T0Z8	OTTHUMG00000014695	ENST00000341865.4:c.519_545delACCTCCCCTGCTGCTGGAACCCCCACC	6.37:g.42075105_42075131delGGTGGGGGTTCCAGCAGCAGGGGAGGT	ENSP00000341368:p.Pro173_Pro181del		42183083	A6NI05	In_Frame_Del	DEL	ENST00000341865.4	37	CCDS47428.1																																																																																				0.665	C6orf132-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040548.2	NM_001164446	
GPRIN2	9721	hgsc.bcm.edu	37	10	46999591	46999592	+	In_Frame_Ins	INS	-	-	ATGAGGGAG	rs112620425	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:46999591_46999592insATGAGGGAG	ENST00000374317.1	+	3	984_985	c.711_712insATGAGGGAG	c.(712-714)atg>ATGAGGGAGatg	p.238_238M>MREM	GPRIN2_ENST00000374314.4_In_Frame_Ins_p.238_238M>MREM	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	238								p.G237_M238insMRE(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						TACTCTGTGGCATGAGGGAGGT	0.629														2399	0.479034	0.4697	0.4856	5008	,	,		38874	0.4782		0.4761	False		,,,				2504	0.4908																1	Insertion - In frame(1)	breast(1)	10								2080,27,2157		11,3,2055,0,24,39						0.9	0.0		dbSNP_130	49	3974,98,4180		16,7,3935,0,91,77	no	codingComplex	GPRIN2	NM_014696.3		27,10,5990,0,115,116	A1A1,A1A2,A1R,A2A2,A2R,RR		49.3456,49.4137,49.3688				6054,125,6337				46419598	SO:0001652	inframe_insertion	9721			BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"""KIAA0514"""	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.712_720dupATGAGGGAG	10.37:g.46999592_46999600dupATGAGGGAG	Exception_encountered		46419597	Q5SVF0	In_Frame_Ins	INS	ENST00000374317.1	37	CCDS31192.1																																																																																				0.629	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
MUC2	4583	hgsc.bcm.edu	37	11	1092802	1092802	+	Frame_Shift_Del	DEL	A	A	-	rs528672869|rs534872608	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:1092802delA	ENST00000441003.2	+	30	4648	c.4621delA	c.(4621-4623)accfs	p.T1545fs	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Frame_Shift_Del_p.T1546fs	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	cactcccatcaccaccaccac	0.627													|||unknown(ALL_OTHER_Ns)	1941	0.38758	0.3911	0.3876	5008	,	,		6166	0.3403		0.3777	False		,,,				2504	0.4417																0			11											25.0	50.0	41.0					11																	1092802		1636	2920	4556	1082802	SO:0001589	frameshift_variant	4583			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4621delA	11.37:g.1092802delA	ENSP00000415183:p.Thr1545fs		1082802	Q14878	Frame_Shift_Del	DEL	ENST00000441003.2	37																																																																																					0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
SAAL1	113174	hgsc.bcm.edu	37	11	18127558	18127559	+	In_Frame_Ins	INS	-	-	CGG	rs74589784|rs72431213|rs148650821	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:18127558_18127559insCGG	ENST00000524803.1	-	1	79_80	c.30_31insCCG	c.(28-33)ccgggt>ccgCCGggt	p.10_11insP	SAAL1_ENST00000533851.1_5'UTR|SAAL1_ENST00000529318.1_In_Frame_Ins_p.10_11insP|SAAL1_ENST00000300013.4_In_Frame_Ins_p.10_11insP			Q96ER3	SAAL1_HUMAN	serum amyloid A-like 1	10				P -> PP (in Ref. 3; AAH12010). {ECO:0000305}.						breast(2)|large_intestine(5)|lung(8)	15						TTGTCGCGACCCGGCGGCGGCG	0.673											OREG0020819	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		734	0.146565	0.0174	0.1556	5008	,	,		17393	0.1349		0.2604	False		,,,				2504	0.2096																0			11																																								18084135	SO:0001652	inframe_insertion	113174			AK123457	CCDS31439.1	11p15.1	2005-10-28			ENSG00000166788	ENSG00000166788			25158	protein-coding gene	gene with protein product							Standard	NM_138421		Approved	FLJ41463	uc001mnq.3	Q96ER3	OTTHUMG00000166428	ENST00000524803.1:c.28_30dupCCG	11.37:g.18127565_18127567dupCGG	ENSP00000432487:p.Pro10_Pro10dup	723	18084134	A6NH05	In_Frame_Ins	INS	ENST00000524803.1	37	CCDS31439.1																																																																																				0.673	SAAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389728.1	NM_138421	
NACA	4666	hgsc.bcm.edu	37	12	57112396	57112464	+	In_Frame_Del	DEL	GGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA	GGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA	-	rs200360816|rs537859542|rs199568239|rs555857821|rs201572567|rs371165343	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	GGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA	GGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:57112396_57112464delGGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA	ENST00000454682.1	-	3	3131_3199	c.2850_2918delTAAAGGAGGCCCAGCTACCCCATCCCCGAAATGGGCCCCCACACCCCCAGCTGCAACTCCTCCCTCCCC	c.(2848-2919)cctaaaggaggcccagctaccccatccccgaaatgggcccccacacccccagctgcaactcctccctcccca>cca	p.950_973PKGGPATPSPKWAPTPPAATPPSP>P	NACA_ENST00000552540.1_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000550952.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000548563.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	950	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P959P(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						ACCTCCTTTTGGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTAGGGGAGGGAG	0.647			T	BCL6	NHL																																			Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	1	Substitution - coding silent(1)	prostate(1)	12																																								55398731	SO:0001651	inframe_deletion	4666			X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.2850_2918delTAAAGGAGGCCCAGCTACCCCATCCCCGAAATGGGCCCCCACACCCCCAGCTGCAACTCCTCCCTCCCC	12.37:g.57112396_57112464delGGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA	ENSP00000403817:p.Pro950_Ser972del		55398663		In_Frame_Del	DEL	ENST00000454682.1	37																																																																																					0.647	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
ORAI1	84876	hgsc.bcm.edu	37	12	122064774	122064779	+	In_Frame_Del	DEL	CCGCCA	CCGCCA	-	rs141919534|rs531278468		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	CCGCCA	CCGCCA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:122064774_122064779delCCGCCA	ENST00000330079.7	+	1	320_325	c.127_132delCCGCCA	c.(127-132)ccgccadel	p.PP47del		NM_032790.3	NP_116179	Q96D31	CRCM1_HUMAN	ORAI calcium release-activated calcium modulator 1	0	Pro-rich.				blood coagulation (GO:0007596)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|regulation of calcium ion transport (GO:0051924)|store-operated calcium entry (GO:0002115)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|store-operated calcium channel activity (GO:0015279)	p.P43_P44delPP(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000415)|Epithelial(86;0.00148)		cccgggggccccgccaccgccaccgc	0.748														5007	0.9998	1.0	1.0	5008	,	,		5795	1.0		1.0	False		,,,				2504	0.999																1	Deletion - In frame(1)	breast(1)	12																																								120549162	SO:0001651	inframe_deletion	84876			AK027372		12q24.31	2014-09-17	2007-08-14	2007-08-14	ENSG00000182500	ENSG00000276045		"""ORAI calcium release-activated calcium modulators"""	25896	protein-coding gene	gene with protein product	"""calcium release-activated calcium modulator 1"""	610277	"""transmembrane protein 142A"""	TMEM142A		16582901	Standard	NM_032790		Approved	FLJ14466, CRACM1	uc021rff.1	Q96D31		ENST00000330079.7:c.127_132delCCGCCA	12.37:g.122064780_122064785delCCGCCA	ENSP00000328216:p.Pro47_Pro48del		120549157	Q3MHV3|Q6DHX2|Q96BP7|Q96K71	In_Frame_Del	DEL	ENST00000330079.7	37	CCDS41851.1																																																																																				0.748	ORAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402151.1	NM_032790	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254148	39254152	+	Frame_Shift_Del	DEL	GGTGG	GGTGG	-	rs201246375		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	GGTGG	GGTGG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:39254148_39254152delGGTGG	ENST00000333822.4	-	1	241_245	c.185_189delCCACC	c.(184-189)cccaccfs	p.PT62fs		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	62	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						GGCGACAGCAGGTGGGCTGGCAGCA	0.649																																																	0			17																																								36507678	SO:0001589	frameshift_variant	728224			AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.185_189delCCACC	17.37:g.39254148_39254152delGGTGG	ENSP00000328444:p.Pro62fs		36507674	A8MSH3	Frame_Shift_Del	DEL	ENST00000333822.4	37	CCDS45674.1																																																																																				0.649	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
HOXB1	3211	hgsc.bcm.edu	37	17	46608184	46608185	+	In_Frame_Ins	INS	-	-	GGGCGCTGT	rs534792734|rs145570960	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:46608184_46608185insGGGCGCTGT	ENST00000239174.6	-	1	174_175	c.82_83insACAGCGCCC	c.(82-84)cca>cACAGCGCCCca	p.27_28insHSA	HOXB1_ENST00000577092.1_In_Frame_Ins_p.27_28insHSA	NM_002144.3	NP_002135.2	P14653	HXB1_HUMAN	homeobox B1	27			A -> AHSA (in allele HOXB1*B). {ECO:0000269|PubMed:10671062, ECO:0000269|PubMed:11091361}.		anatomical structure formation involved in morphogenesis (GO:0048646)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|multicellular organismal development (GO:0007275)|pattern specification process (GO:0007389)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding (GO:0043565)	p.A27_P28insHSA(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						AAAGGAGGTTGGGGCGCTGTGG	0.619														667	0.133187	0.1157	0.1225	5008	,	,		17469	0.0982		0.2008	False		,,,				2504	0.1309																1	Insertion - In frame(1)	lung(1)	17								528,3732		33,462,1635						4.2	1.0		dbSNP_134	66	1685,6565		171,1343,2611	no	coding	HOXB1	NM_002144.3		204,1805,4246	A1A1,A1R,RR		20.4242,12.3944,17.6898				2213,10297				43963184	SO:0001652	inframe_insertion	3211				CCDS32675.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120094	ENSG00000120094		"""Homeoboxes / ANTP class : HOXL subclass"""	5111	protein-coding gene	gene with protein product		142968	"""homeo box B1"""	HOX2, HOX2I		1973146, 1358459	Standard	NM_002144		Approved		uc002ink.1	P14653	OTTHUMG00000159929	ENST00000239174.6:c.74_82dupACAGCGCCC	17.37:g.46608185_46608193dupGGGCGCTGT	ENSP00000355140:p.His25_Ala27dup		43963183	Q4VB03	In_Frame_Ins	INS	ENST00000239174.6	37	CCDS32675.1																																																																																				0.619	HOXB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358383.3		
SF3A2	8175	hgsc.bcm.edu	37	19	2248165	2248185	+	In_Frame_Del	DEL	CCAGCCCCCGGGGTTCACCCA	CCAGCCCCCGGGGTTCACCCA	-	rs144349304|rs138163109		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	CCAGCCCCCGGGGTTCACCCA	CCAGCCCCCGGGGTTCACCCA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:2248165_2248185delCCAGCCCCCGGGGTTCACCCA	ENST00000221494.5	+	9	1433_1453	c.1015_1035delCCAGCCCCCGGGGTTCACCCA	c.(1015-1035)ccagcccccggggttcacccadel	p.PAPGVHP360del	AMH_ENST00000221496.4_5'Flank|MIR4321_ENST00000592276.1_RNA	NM_007165.4	NP_009096.2	Q15428	SF3A2_HUMAN	splicing factor 3a, subunit 2, 66kDa	360	Pro-rich.				gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGTCCACCCTCCAGCCCCCGGGGTTCACCCACCAGCCCCCG	0.742																																																	0			19								62,2436		14,34,1201						-6.4	0.0			3	497,5077		113,271,2403	no	coding	SF3A2	NM_007165.4		127,305,3604	A1A1,A1R,RR		8.9164,2.482,6.9252				559,7513				2199185	SO:0001651	inframe_deletion	8175			L21990	CCDS12084.1	19p13.3	2012-10-02	2002-08-29		ENSG00000104897	ENSG00000104897			10766	protein-coding gene	gene with protein product		600796	"""splicing factor 3a, subunit 2, 66kD"""			8211113, 8541848	Standard	NM_007165		Approved	SF3a66, SAP62, PRPF11, Prp11	uc002lvg.3	Q15428	OTTHUMG00000180414	ENST00000221494.5:c.1015_1035delCCAGCCCCCGGGGTTCACCCA	19.37:g.2248165_2248185delCCAGCCCCCGGGGTTCACCCA	ENSP00000221494:p.Pro360_Pro366del		2199165	B2RBU1|D6W605|O75245	In_Frame_Del	DEL	ENST00000221494.5	37	CCDS12084.1																																																																																				0.742	SF3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451268.3		
LSR	51599	hgsc.bcm.edu	37	19	35758275	35758276	+	In_Frame_Ins	INS	-	-	GGA	rs397751431|rs79703261|rs35939322|rs142507475		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:35758275_35758276insGGA	ENST00000361790.3	+	9	1711_1712	c.1552_1553insGGA	c.(1552-1554)ggg>gGGAgg	p.519_520insR	USF2_ENST00000594064.1_5'Flank|LSR_ENST00000602122.1_In_Frame_Ins_p.499_500insR|LSR_ENST00000347609.4_In_Frame_Ins_p.461_462insR|LSR_ENST00000354900.3_In_Frame_Ins_p.500_501insR|LSR_ENST00000427250.1_In_Frame_Ins_p.363_364insR|AD000684.2_ENST00000602262.1_RNA|USF2_ENST00000343550.5_5'Flank|USF2_ENST00000595068.1_5'Flank|LSR_ENST00000360798.3_In_Frame_Ins_p.451_452insR|USF2_ENST00000222305.3_5'Flank|USF2_ENST00000379134.3_5'Flank	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	519					embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GAGTAATGGTGGGAGAAGCCGG	0.723																																																	0			19							,,	2087,1919		640,807,556					,,	0.2	0.7		dbSNP_130	14	5961,1881		2351,1259,311	no	coding,coding,coding	LSR	NM_205835.2,NM_205834.2,NM_015925.5	,,	2991,2066,867	A1A1,A1R,RR		23.9862,47.9031,32.0729	,,	,,		8048,3800				40450116	SO:0001652	inframe_insertion	51599			AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29572	protein-coding gene	gene with protein product	"""lipolysis-stimulated remnant"", ""immunoglobulin-like domain containing receptor 3"""					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.1553_1555dupGGA	19.37:g.35758276_35758278dupGGA	ENSP00000354575:p.Arg520_Arg521dup		40450115	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	In_Frame_Ins	INS	ENST00000361790.3	37	CCDS12450.1																																																																																				0.723	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925	
SPINT2	10653	hgsc.bcm.edu	37	19	38780921	38780921	+	Splice_Site	DEL	G	G	-			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:38780921delG	ENST00000301244.7	+	5	988		c.e5+1		SPINT2_ENST00000454580.3_Splice_Site|SPINT2_ENST00000587090.1_Splice_Site|CTB-102L5.4_ENST00000591889.1_Splice_Site	NM_021102.3	NP_066925.1	O43291	SPIT2_HUMAN	serine peptidase inhibitor, Kunitz type, 2						cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			large_intestine(2)|lung(1)|ovary(1)	4	all_cancers(60;6.83e-07)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CGCTGCTTCCGTAAGTCTGCA	0.572																																																	0			19											34.0	36.0	35.0					19																	38780921		2203	4300	6503	43472761	SO:0001630	splice_region_variant	10653			U78095	CCDS12510.1, CCDS54261.1	19q13.2	2010-05-12	2005-08-17		ENSG00000167642	ENSG00000167642			11247	protein-coding gene	gene with protein product	"""placental bikunin"""	605124	"""serine protease inhibitor, Kunitz type, 2"""			9115294, 9346890	Standard	NM_021102		Approved	Kop, HAI-2	uc002ohr.2	O43291		ENST00000301244.7:c.553+1G>-	19.37:g.38780921delG			43472761	A8K667|B4DLU1|O00271|O14895|Q5TZQ3|Q969E0	Frame_Shift_Del	DEL	ENST00000301244.7	37	CCDS12510.1																																																																																				0.572	SPINT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458151.2		Intron
KRTAP10-7	386675	hgsc.bcm.edu	37	21	46020656	46020670	+	In_Frame_Del	DEL	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG	-	rs36208679|rs60739860|rs373191083		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr21:46020656_46020670delCTGCTGCGCCCCCAG	ENST00000380102.2	+	1	160_174	c.135_149delCTGCTGCGCCCCCAG	c.(133-150)ccctgctgcgcccccagc>ccc	p.CCAPS46del	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	46	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.S50_P54delSCCAP(1)		breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						GCGAGCCCCCCTGCTGCGCCCCCAGCTGCTGCGCC	0.698																																																	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	21							,	2258,1042		849,560,241					,	-0.7	1.0		dbSNP_126	22	6001,1123		2605,791,166	no	coding,intron	TSPEAR,KRTAP10-7	NM_198689.2,NM_144991.2	,	3454,1351,407	A1A1,A1R,RR		15.7636,31.5758,20.7694	,	,		8259,2165				44845098	SO:0001651	inframe_deletion	386675			AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"""Keratin associated proteins"""	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.135_149delCTGCTGCGCCCCCAG	21.37:g.46020656_46020670delCTGCTGCGCCCCCAG	ENSP00000369445:p.Cys46_Ser50del		44845084	Q0VDJ8|Q70LJ2	Frame_Shift_Del	DEL	ENST00000380102.2	37																																																																																					0.698	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689	
NEFH	4744	hgsc.bcm.edu	37	22	29885599	29885604	+	In_Frame_Del	DEL	AGGAAG	AGGAAG	-	rs267607534|rs373980795|rs267607533|rs149571560|rs200984527|rs370803228		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	AGGAAG	AGGAAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr22:29885599_29885604delAGGAAG	ENST00000310624.6	+	4	2003_2008	c.1970_1975delAGGAAG	c.(1969-1977)aaggaagag>aag	p.EE658del		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	664	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						TCCCCAGAGAAGGAAGAGGCCAAGTC	0.558																																																	0			22																																								28215604	SO:0001651	inframe_deletion	4744				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1970_1975delAGGAAG	22.37:g.29885599_29885604delAGGAAG	ENSP00000311997:p.Glu658_Glu659del		28215599	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Del	DEL	ENST00000310624.6	37	CCDS13858.1																																																																																				0.558	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
ADM2	79924	hgsc.bcm.edu	37	22	50921149	50921166	+	In_Frame_Del	DEL	ACACTCGGGCCCCCGAAG	ACACTCGGGCCCCCGAAG	-	rs559809485|rs72438078|rs3840963|rs199649182	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	ACACTCGGGCCCCCGAAG	ACACTCGGGCCCCCGAAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr22:50921149_50921166delACACTCGGGCCCCCGAAG	ENST00000395738.2	+	2	556_573	c.264_281delACACTCGGGCCCCCGAAG	c.(262-282)caacactcgggcccccgaaga>caa	p.HSGPRR95del	ADM2_ENST00000362068.2_In_Frame_Del_p.TRAPED6del|ADM2_ENST00000395737.1_In_Frame_Del_p.HSGPRR95del	NM_001253845.1|NM_024866.5	NP_001240774.1|NP_079142.2	Q7Z4H4	ADM2_HUMAN	adrenomedullin 2	95					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|digestion (GO:0007586)|feeding behavior (GO:0007631)|negative regulation of blood pressure (GO:0045776)|positive regulation of angiogenesis (GO:0045766)|positive regulation of gene expression (GO:0010628)|protein phosphorylation (GO:0006468)	extracellular region (GO:0005576)	protein complex binding (GO:0032403)	p.H95_R100delHSGPRR(1)		breast(1)|kidney(1)	2		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GTGGCCGCCAACACTCGGGCCCCCGAAGACACTCGGGC	0.693														589	0.117612	0.0968	0.1686	5008	,	,		17047	0.1915		0.1213	False		,,,				2504	0.0297																1	Deletion - In frame(1)	breast(1)	22								288,3296		54,180,1558						2.4	0.0		dbSNP_130	10	572,6758		74,424,3167	no	coding	ADM2	NM_024866.4		128,604,4725	A1A1,A1R,RR		7.8035,8.0357,7.8798				860,10054				49268032	SO:0001651	inframe_deletion	79924			AF529213	CCDS33682.1	22q13.33	2013-02-25			ENSG00000128165	ENSG00000128165		"""Endogenous ligands"""	28898	protein-coding gene	gene with protein product		608682				14706825	Standard	NM_024866		Approved	AM2, FLJ21135	uc003blj.3	Q7Z4H4	OTTHUMG00000150202	ENST00000395738.2:c.264_281delACACTCGGGCCCCCGAAG	22.37:g.50921149_50921166delACACTCGGGCCCCCGAAG	ENSP00000379087:p.His95_Arg100del		49268015	Q3LFQ0	In_Frame_Del	DEL	ENST00000395738.2	37	CCDS33682.1																																																																																				0.693	ADM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316816.1	NM_024866	
LCE4A	199834	hgsc.bcm.edu	37	1	152681680	152681681	+	In_Frame_Ins	INS	-	-	AGCTCTGGGGGCTGCTGT	rs6143428|rs11269814|rs200890315|rs33921874	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:152681680_152681681insAGCTCTGGGGGCTGCTGT	ENST00000368777.1	+	2	385_386	c.129_130insAGCTCTGGGGGCTGCTGT	c.(130-132)agc>AGCTCTGGGGGCTGCTGTagc	p.44_44S>SSGGCCS	LCE4A_ENST00000335535.3_In_Frame_Ins_p.44_44S>SSGGCCS			Q5TA78	LCE4A_HUMAN	late cornified envelope 4A	44	Cys-rich.				keratinization (GO:0031424)					endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.116)			GCTGTGGCTCCAGCTCTGGGGG	0.599														4009	0.800519	0.9758	0.853	5008	,	,		18534	0.6855		0.7177	False		,,,				2504	0.7301																0			1																																								150948305	SO:0001652	inframe_insertion	199834			BI670517	CCDS1022.1	1q22	2008-02-05	2004-10-11	2004-10-15	ENSG00000187170	ENSG00000187170		"""Late cornified envelopes"""	16613	protein-coding gene	gene with protein product		612618	"""small proline rich-like (epidermal differentiation complex) 4A"""	SPRL4A		11698679	Standard	NM_178356		Approved	LEP8	uc001fak.2	Q5TA78	OTTHUMG00000014394	Exception_encountered	1.37:g.152681680_152681681insAGCTCTGGGGGCTGCTGT	Exception_encountered		150948304	Q14D97	In_Frame_Ins	INS	ENST00000368777.1	37	CCDS1022.1																																																																																				0.599	LCE4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040048.1	NM_178356	
PRG4	10216	hgsc.bcm.edu	37	1	186276284	186276286	+	In_Frame_Del	DEL	CTC	CTC	-	rs200031345|rs145095882|rs143141440	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	CTC	CTC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr1:186276284_186276286delCTC	ENST00000445192.2	+	7	1478_1480	c.1433_1435delCTC	c.(1432-1437)actccc>acc	p.P479del	PRG4_ENST00000367483.4_In_Frame_Del_p.P438del|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367485.4_In_Frame_Del_p.P386del|PRG4_ENST00000367486.3_In_Frame_Del_p.P436del	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	479	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.P479delP(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						GCACCCACCACTCCCAAAGAGCC	0.65																																																	1	Deletion - In frame(1)	large_intestine(1)	1							,,,	348,3912		14,320,1796					,,,	-1.4	0.0			89	1023,7215		71,881,3167	no	coding,coding,coding,coding	PRG4	NM_005807.3,NM_001127710.1,NM_001127709.1,NM_001127708.1	,,,	85,1201,4963	A1A1,A1R,RR		12.4181,8.169,10.9698	,,,	,,,		1371,11127				184542909	SO:0001651	inframe_deletion	23572			U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1433_1435delCTC	1.37:g.186276284_186276286delCTC	ENSP00000399679:p.Pro479del		184542907	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	In_Frame_Del	DEL	ENST00000445192.2	37	CCDS1369.1																																																																																				0.650	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
PRKRA	8575	hgsc.bcm.edu	37	2	179315735	179315736	+	Frame_Shift_Del	DEL	GC	GC	-	rs141354030|rs79769305	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	GC	GC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr2:179315735_179315736delGC	ENST00000325748.4	-	1	222_223	c.22_23delGC	c.(22-24)gccfs	p.A8fs	PRKRA_ENST00000487082.1_5'Flank|DFNB59_ENST00000375129.4_5'Flank|PRKRA_ENST00000432031.2_5'Flank|PRKRA_ENST00000438687.3_5'UTR|DFNB59_ENST00000409117.3_5'Flank|PRKRA_ENST00000470200.1_5'UTR	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator	8	Sufficient for self-association and interaction with TARBP2.				cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			CGGGGCCTCGGCGCGGTGCCTG	0.757														1193	0.238219	0.1649	0.3545	5008	,	,		12129	0.123		0.339	False		,,,				2504	0.2699				Melanoma(200;68 3001 23825 48764)												0			2								658,2174		225,208,983						-1.9	0.8		dbSNP_134	7	2206,4138		751,704,1717	no	frameshift	PRKRA	NM_003690.4		976,912,2700	A1A1,A1R,RR		34.773,23.2345,31.2119				2864,6312				179023982	SO:0001589	frameshift_variant	8575			AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"""protein activator of the interferon-induced protein kinase"""	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.22_23delGC	2.37:g.179315737_179315738delGC	ENSP00000318176:p.Ala8fs		179023981	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Frame_Shift_Del	DEL	ENST00000325748.4	37	CCDS2279.1																																																																																				0.757	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690	
MUC4	4585	hgsc.bcm.edu	37	3	195508202	195508249	+	In_Frame_Del	DEL	CTGAGGAAGGGCTAGTGACAGGAAGAGGCATGGTGTCACCTGTGGATA	CTGAGGAAGGGCTAGTGACAGGAAGAGGCATGGTGTCACCTGTGGATA	-	rs558318316|rs199592227|rs566665732|rs144373027|rs138141889|rs542067128|rs144420167|rs576510701|rs533775458|rs200984123|rs537584428|rs201826718|rs536470139|rs574664481|rs201846606	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	CTGAGGAAGGGCTAGTGACAGGAAGAGGCATGGTGTCACCTGTGGATA	CTGAGGAAGGGCTAGTGACAGGAAGAGGCATGGTGTCACCTGTGGATA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:195508202_195508249delCTGAGGAAGGGCTAGTGACAGGAAGAGGCATGGTGTCACCTGTGGATA	ENST00000463781.3	-	2	10661_10708	c.10202_10249delTATCCACAGGTGACACCATGCCTCTTCCTGTCACTAGCCCTTCCTCAG	c.(10201-10251)gtatccacaggtgacaccatgcctcttcctgtcactagcccttcctcagca>gca	p.VSTGDTMPLPVTSPSS3401del	MUC4_ENST00000475231.1_In_Frame_Del_p.VSTGDTMPLPVTSPSS3401del|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V3401A(3)|p.P3408R(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CCTGTGGATGCTGAGGAAGGGCTAGTGACAGGAAGAGGCATGGTGTCACCTGTGGATACTGAGGAAGT	0.585																																																	4	Substitution - Missense(4)	stomach(2)|kidney(1)|endometrium(1)	3							,,	191,3561		48,95,1733					,,	-0.4	0.0			12	700,6748		140,420,3164	no	intron,coding,intron	MUC4	NM_138297.4,NM_018406.6,NM_004532.5	,,	188,515,4897	A1A1,A1R,RR		9.3985,5.0906,7.9554	,,	,,		891,10309				196993028	SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10202_10249delTATCCACAGGTGACACCATGCCTCTTCCTGTCACTAGCCCTTCCTCAG	3.37:g.195508202_195508249delCTGAGGAAGGGCTAGTGACAGGAAGAGGCATGGTGTCACCTGTGGATA	ENSP00000417498:p.Val3401_Ser3416del		196992981	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				0.585	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195515367	195515414	+	In_Frame_Del	DEL	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	-	rs369312980|rs547775645|rs201510137|rs200193644|rs531942134|rs13060431|rs200400545|rs71180964|rs199583597|rs55868431|rs55803325|rs550428312|rs199702053|rs13065584	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr3:195515367_195515414delGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	ENST00000463781.3	-	2	3496_3543	c.3037_3084delAGCCCTTCCTCAGTATCCACAGGTCACACCACCCCTCTTCCTGTCACC	c.(3037-3084)agcccttcctcagtatccacaggtcacaccacccctcttcctgtcaccdel	p.SPSSVSTGHTTPLPVT1013del	MUC4_ENST00000475231.1_In_Frame_Del_p.SPSSVSTGHTTPLPVT1013del|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	448	Repeat.|Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1013_T1028delSPSSVSTGHTTPLPVT(4)|p.S1013G(2)|p.T1022A(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGTGTCGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCTGGTGACAGGA	0.573																																																	8	Substitution - Missense(4)|Deletion - In frame(4)	stomach(6)|prostate(2)	3																																								196999809	SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3037_3084delAGCCCTTCCTCAGTATCCACAGGTCACACCACCCCTCTTCCTGTCACC	3.37:g.195515367_195515414delGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	ENSP00000417498:p.Ser1013_Thr1028del		196999762	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				0.573	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388504	1388505	+	Frame_Shift_Del	DEL	CG	CG	-	rs568118449|rs528384190|rs115485610	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	CG	CG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr4:1388504_1388505delCG	ENST00000324803.4	+	1	3165_3166	c.205_206delCG	c.(205-207)cgtfs	p.R69fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	69					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			TGCTCACACACGTGTCCATGTG	0.629														54	0.0107827	0.0174	0.0043	5008	,	,		20699	0.002		0.0169	False		,,,				2504	0.0092																0			4																																								1378505	SO:0001589	frameshift_variant	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.205_206delCG	4.37:g.1388504_1388505delCG	ENSP00000323978:p.Arg69fs		1378504	Q8NB03	Frame_Shift_Del	DEL	ENST00000324803.4	37	CCDS3349.1																																																																																				0.629	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
GPRIN2	9721	hgsc.bcm.edu	37	10	46999591	46999592	+	In_Frame_Ins	INS	-	-	ATGAGGGAG	rs112620425	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr10:46999591_46999592insATGAGGGAG	ENST00000374317.1	+	3	984_985	c.711_712insATGAGGGAG	c.(712-714)atg>ATGAGGGAGatg	p.238_238M>MREM	GPRIN2_ENST00000374314.4_In_Frame_Ins_p.238_238M>MREM	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	238								p.G237_M238insMRE(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						TACTCTGTGGCATGAGGGAGGT	0.629														2399	0.479034	0.4697	0.4856	5008	,	,		38874	0.4782		0.4761	False		,,,				2504	0.4908																1	Insertion - In frame(1)	breast(1)	10								2080,27,2157		11,3,2055,0,24,39						0.9	0.0		dbSNP_130	49	3974,98,4180		16,7,3935,0,91,77	no	codingComplex	GPRIN2	NM_014696.3		27,10,5990,0,115,116	A1A1,A1A2,A1R,A2A2,A2R,RR		49.3456,49.4137,49.3688				6054,125,6337				46419598	SO:0001652	inframe_insertion	9721			BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"""KIAA0514"""	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.712_720dupATGAGGGAG	10.37:g.46999592_46999600dupATGAGGGAG	Exception_encountered		46419597	Q5SVF0	In_Frame_Ins	INS	ENST00000374317.1	37	CCDS31192.1																																																																																				0.629	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
MUC2	4583	hgsc.bcm.edu	37	11	1092802	1092802	+	Frame_Shift_Del	DEL	A	A	-	rs528672869|rs534872608	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:1092802delA	ENST00000441003.2	+	30	4648	c.4621delA	c.(4621-4623)accfs	p.T1545fs	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Frame_Shift_Del_p.T1546fs	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	cactcccatcaccaccaccac	0.627													|||unknown(ALL_OTHER_Ns)	1941	0.38758	0.3911	0.3876	5008	,	,		6166	0.3403		0.3777	False		,,,				2504	0.4417																0			11											25.0	50.0	41.0					11																	1092802		1636	2920	4556	1082802	SO:0001589	frameshift_variant	4583			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4621delA	11.37:g.1092802delA	ENSP00000415183:p.Thr1545fs		1082802	Q14878	Frame_Shift_Del	DEL	ENST00000441003.2	37																																																																																					0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
SAAL1	113174	hgsc.bcm.edu	37	11	18127558	18127559	+	In_Frame_Ins	INS	-	-	CGG	rs74589784|rs72431213|rs148650821	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr11:18127558_18127559insCGG	ENST00000524803.1	-	1	79_80	c.30_31insCCG	c.(28-33)ccgggt>ccgCCGggt	p.10_11insP	SAAL1_ENST00000533851.1_5'UTR|SAAL1_ENST00000529318.1_In_Frame_Ins_p.10_11insP|SAAL1_ENST00000300013.4_In_Frame_Ins_p.10_11insP			Q96ER3	SAAL1_HUMAN	serum amyloid A-like 1	10				P -> PP (in Ref. 3; AAH12010). {ECO:0000305}.						breast(2)|large_intestine(5)|lung(8)	15						TTGTCGCGACCCGGCGGCGGCG	0.673											OREG0020819	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		734	0.146565	0.0174	0.1556	5008	,	,		17393	0.1349		0.2604	False		,,,				2504	0.2096																0			11																																								18084135	SO:0001652	inframe_insertion	113174			AK123457	CCDS31439.1	11p15.1	2005-10-28			ENSG00000166788	ENSG00000166788			25158	protein-coding gene	gene with protein product							Standard	NM_138421		Approved	FLJ41463	uc001mnq.3	Q96ER3	OTTHUMG00000166428	ENST00000524803.1:c.28_30dupCCG	11.37:g.18127565_18127567dupCGG	ENSP00000432487:p.Pro10_Pro10dup	723	18084134	A6NH05	In_Frame_Ins	INS	ENST00000524803.1	37	CCDS31439.1																																																																																				0.673	SAAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389728.1	NM_138421	
NACA	4666	hgsc.bcm.edu	37	12	57112396	57112464	+	In_Frame_Del	DEL	GGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA	GGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA	-	rs200360816|rs537859542|rs199568239|rs555857821|rs201572567|rs371165343	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	GGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA	GGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:57112396_57112464delGGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA	ENST00000454682.1	-	3	3131_3199	c.2850_2918delTAAAGGAGGCCCAGCTACCCCATCCCCGAAATGGGCCCCCACACCCCCAGCTGCAACTCCTCCCTCCCC	c.(2848-2919)cctaaaggaggcccagctaccccatccccgaaatgggcccccacacccccagctgcaactcctccctcccca>cca	p.950_973PKGGPATPSPKWAPTPPAATPPSP>P	NACA_ENST00000552540.1_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000550952.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000548563.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	950	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P959P(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						ACCTCCTTTTGGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTAGGGGAGGGAG	0.647			T	BCL6	NHL																																			Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	1	Substitution - coding silent(1)	prostate(1)	12																																								55398731	SO:0001651	inframe_deletion	4666			X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.2850_2918delTAAAGGAGGCCCAGCTACCCCATCCCCGAAATGGGCCCCCACACCCCCAGCTGCAACTCCTCCCTCCCC	12.37:g.57112396_57112464delGGGGAGGGAGGAGTTGCAGCTGGGGGTGTGGGGGCCCATTTCGGGGATGGGGTAGCTGGGCCTCCTTTA	ENSP00000403817:p.Pro950_Ser972del		55398663		In_Frame_Del	DEL	ENST00000454682.1	37																																																																																					0.647	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
ORAI1	84876	hgsc.bcm.edu	37	12	122064774	122064779	+	In_Frame_Del	DEL	CCGCCA	CCGCCA	-	rs141919534|rs531278468		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	CCGCCA	CCGCCA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr12:122064774_122064779delCCGCCA	ENST00000330079.7	+	1	320_325	c.127_132delCCGCCA	c.(127-132)ccgccadel	p.PP47del		NM_032790.3	NP_116179	Q96D31	CRCM1_HUMAN	ORAI calcium release-activated calcium modulator 1	0	Pro-rich.				blood coagulation (GO:0007596)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|regulation of calcium ion transport (GO:0051924)|store-operated calcium entry (GO:0002115)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|store-operated calcium channel activity (GO:0015279)	p.P43_P44delPP(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000415)|Epithelial(86;0.00148)		cccgggggccccgccaccgccaccgc	0.748														5007	0.9998	1.0	1.0	5008	,	,		5795	1.0		1.0	False		,,,				2504	0.999																1	Deletion - In frame(1)	breast(1)	12																																								120549162	SO:0001651	inframe_deletion	84876			AK027372		12q24.31	2014-09-17	2007-08-14	2007-08-14	ENSG00000182500	ENSG00000276045		"""ORAI calcium release-activated calcium modulators"""	25896	protein-coding gene	gene with protein product	"""calcium release-activated calcium modulator 1"""	610277	"""transmembrane protein 142A"""	TMEM142A		16582901	Standard	NM_032790		Approved	FLJ14466, CRACM1	uc021rff.1	Q96D31		ENST00000330079.7:c.127_132delCCGCCA	12.37:g.122064780_122064785delCCGCCA	ENSP00000328216:p.Pro47_Pro48del		120549157	Q3MHV3|Q6DHX2|Q96BP7|Q96K71	In_Frame_Del	DEL	ENST00000330079.7	37	CCDS41851.1																																																																																				0.748	ORAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402151.1	NM_032790	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254148	39254152	+	Frame_Shift_Del	DEL	GGTGG	GGTGG	-	rs201246375		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	GGTGG	GGTGG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:39254148_39254152delGGTGG	ENST00000333822.4	-	1	241_245	c.185_189delCCACC	c.(184-189)cccaccfs	p.PT62fs		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	62	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						GGCGACAGCAGGTGGGCTGGCAGCA	0.649																																																	0			17																																								36507678	SO:0001589	frameshift_variant	728224			AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.185_189delCCACC	17.37:g.39254148_39254152delGGTGG	ENSP00000328444:p.Pro62fs		36507674	A8MSH3	Frame_Shift_Del	DEL	ENST00000333822.4	37	CCDS45674.1																																																																																				0.649	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
HOXB1	3211	hgsc.bcm.edu	37	17	46608184	46608185	+	In_Frame_Ins	INS	-	-	GGGCGCTGT	rs534792734|rs145570960	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr17:46608184_46608185insGGGCGCTGT	ENST00000239174.6	-	1	174_175	c.82_83insACAGCGCCC	c.(82-84)cca>cACAGCGCCCca	p.27_28insHSA	HOXB1_ENST00000577092.1_In_Frame_Ins_p.27_28insHSA	NM_002144.3	NP_002135.2	P14653	HXB1_HUMAN	homeobox B1	27			A -> AHSA (in allele HOXB1*B). {ECO:0000269|PubMed:10671062, ECO:0000269|PubMed:11091361}.		anatomical structure formation involved in morphogenesis (GO:0048646)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|multicellular organismal development (GO:0007275)|pattern specification process (GO:0007389)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding (GO:0043565)	p.A27_P28insHSA(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						AAAGGAGGTTGGGGCGCTGTGG	0.619														667	0.133187	0.1157	0.1225	5008	,	,		17469	0.0982		0.2008	False		,,,				2504	0.1309																1	Insertion - In frame(1)	lung(1)	17								528,3732		33,462,1635						4.2	1.0		dbSNP_134	66	1685,6565		171,1343,2611	no	coding	HOXB1	NM_002144.3		204,1805,4246	A1A1,A1R,RR		20.4242,12.3944,17.6898				2213,10297				43963184	SO:0001652	inframe_insertion	3211				CCDS32675.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120094	ENSG00000120094		"""Homeoboxes / ANTP class : HOXL subclass"""	5111	protein-coding gene	gene with protein product		142968	"""homeo box B1"""	HOX2, HOX2I		1973146, 1358459	Standard	NM_002144		Approved		uc002ink.1	P14653	OTTHUMG00000159929	ENST00000239174.6:c.74_82dupACAGCGCCC	17.37:g.46608185_46608193dupGGGCGCTGT	ENSP00000355140:p.His25_Ala27dup		43963183	Q4VB03	In_Frame_Ins	INS	ENST00000239174.6	37	CCDS32675.1																																																																																				0.619	HOXB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358383.3		
SF3A2	8175	hgsc.bcm.edu	37	19	2248165	2248185	+	In_Frame_Del	DEL	CCAGCCCCCGGGGTTCACCCA	CCAGCCCCCGGGGTTCACCCA	-	rs144349304|rs138163109		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	CCAGCCCCCGGGGTTCACCCA	CCAGCCCCCGGGGTTCACCCA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:2248165_2248185delCCAGCCCCCGGGGTTCACCCA	ENST00000221494.5	+	9	1433_1453	c.1015_1035delCCAGCCCCCGGGGTTCACCCA	c.(1015-1035)ccagcccccggggttcacccadel	p.PAPGVHP360del	AMH_ENST00000221496.4_5'Flank|MIR4321_ENST00000592276.1_RNA	NM_007165.4	NP_009096.2	Q15428	SF3A2_HUMAN	splicing factor 3a, subunit 2, 66kDa	360	Pro-rich.				gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGTCCACCCTCCAGCCCCCGGGGTTCACCCACCAGCCCCCG	0.742																																																	0			19								62,2436		14,34,1201						-6.4	0.0			3	497,5077		113,271,2403	no	coding	SF3A2	NM_007165.4		127,305,3604	A1A1,A1R,RR		8.9164,2.482,6.9252				559,7513				2199185	SO:0001651	inframe_deletion	8175			L21990	CCDS12084.1	19p13.3	2012-10-02	2002-08-29		ENSG00000104897	ENSG00000104897			10766	protein-coding gene	gene with protein product		600796	"""splicing factor 3a, subunit 2, 66kD"""			8211113, 8541848	Standard	NM_007165		Approved	SF3a66, SAP62, PRPF11, Prp11	uc002lvg.3	Q15428	OTTHUMG00000180414	ENST00000221494.5:c.1015_1035delCCAGCCCCCGGGGTTCACCCA	19.37:g.2248165_2248185delCCAGCCCCCGGGGTTCACCCA	ENSP00000221494:p.Pro360_Pro366del		2199165	B2RBU1|D6W605|O75245	In_Frame_Del	DEL	ENST00000221494.5	37	CCDS12084.1																																																																																				0.742	SF3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451268.3		
LSR	51599	hgsc.bcm.edu	37	19	35758275	35758276	+	In_Frame_Ins	INS	-	-	GGA	rs397751431|rs79703261|rs35939322|rs142507475		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:35758275_35758276insGGA	ENST00000361790.3	+	9	1711_1712	c.1552_1553insGGA	c.(1552-1554)ggg>gGGAgg	p.519_520insR	USF2_ENST00000594064.1_5'Flank|LSR_ENST00000602122.1_In_Frame_Ins_p.499_500insR|LSR_ENST00000347609.4_In_Frame_Ins_p.461_462insR|LSR_ENST00000354900.3_In_Frame_Ins_p.500_501insR|LSR_ENST00000427250.1_In_Frame_Ins_p.363_364insR|AD000684.2_ENST00000602262.1_RNA|USF2_ENST00000343550.5_5'Flank|USF2_ENST00000595068.1_5'Flank|LSR_ENST00000360798.3_In_Frame_Ins_p.451_452insR|USF2_ENST00000222305.3_5'Flank|USF2_ENST00000379134.3_5'Flank	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	519					embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GAGTAATGGTGGGAGAAGCCGG	0.723																																																	0			19							,,	2087,1919		640,807,556					,,	0.2	0.7		dbSNP_130	14	5961,1881		2351,1259,311	no	coding,coding,coding	LSR	NM_205835.2,NM_205834.2,NM_015925.5	,,	2991,2066,867	A1A1,A1R,RR		23.9862,47.9031,32.0729	,,	,,		8048,3800				40450116	SO:0001652	inframe_insertion	51599			AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29572	protein-coding gene	gene with protein product	"""lipolysis-stimulated remnant"", ""immunoglobulin-like domain containing receptor 3"""					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.1553_1555dupGGA	19.37:g.35758276_35758278dupGGA	ENSP00000354575:p.Arg520_Arg521dup		40450115	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	In_Frame_Ins	INS	ENST00000361790.3	37	CCDS12450.1																																																																																				0.723	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925	
SPINT2	10653	hgsc.bcm.edu	37	19	38780921	38780921	+	Splice_Site	DEL	G	G	-			TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr19:38780921delG	ENST00000301244.7	+	5	988		c.e5+1		SPINT2_ENST00000454580.3_Splice_Site|SPINT2_ENST00000587090.1_Splice_Site|CTB-102L5.4_ENST00000591889.1_Splice_Site	NM_021102.3	NP_066925.1	O43291	SPIT2_HUMAN	serine peptidase inhibitor, Kunitz type, 2						cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			large_intestine(2)|lung(1)|ovary(1)	4	all_cancers(60;6.83e-07)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CGCTGCTTCCGTAAGTCTGCA	0.572																																																	0			19											34.0	36.0	35.0					19																	38780921		2203	4300	6503	43472761	SO:0001630	splice_region_variant	10653			U78095	CCDS12510.1, CCDS54261.1	19q13.2	2010-05-12	2005-08-17		ENSG00000167642	ENSG00000167642			11247	protein-coding gene	gene with protein product	"""placental bikunin"""	605124	"""serine protease inhibitor, Kunitz type, 2"""			9115294, 9346890	Standard	NM_021102		Approved	Kop, HAI-2	uc002ohr.2	O43291		ENST00000301244.7:c.553+1G>-	19.37:g.38780921delG			43472761	A8K667|B4DLU1|O00271|O14895|Q5TZQ3|Q969E0	Frame_Shift_Del	DEL	ENST00000301244.7	37	CCDS12510.1																																																																																				0.572	SPINT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458151.2		Intron
KRTAP10-7	386675	hgsc.bcm.edu	37	21	46020656	46020670	+	In_Frame_Del	DEL	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG	-	rs36208679|rs60739860|rs373191083		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr21:46020656_46020670delCTGCTGCGCCCCCAG	ENST00000380102.2	+	1	160_174	c.135_149delCTGCTGCGCCCCCAG	c.(133-150)ccctgctgcgcccccagc>ccc	p.CCAPS46del	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	46	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.S50_P54delSCCAP(1)		breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						GCGAGCCCCCCTGCTGCGCCCCCAGCTGCTGCGCC	0.698																																																	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	21							,	2258,1042		849,560,241					,	-0.7	1.0		dbSNP_126	22	6001,1123		2605,791,166	no	coding,intron	TSPEAR,KRTAP10-7	NM_198689.2,NM_144991.2	,	3454,1351,407	A1A1,A1R,RR		15.7636,31.5758,20.7694	,	,		8259,2165				44845098	SO:0001651	inframe_deletion	386675			AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"""Keratin associated proteins"""	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.135_149delCTGCTGCGCCCCCAG	21.37:g.46020656_46020670delCTGCTGCGCCCCCAG	ENSP00000369445:p.Cys46_Ser50del		44845084	Q0VDJ8|Q70LJ2	Frame_Shift_Del	DEL	ENST00000380102.2	37																																																																																					0.698	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689	
NEFH	4744	hgsc.bcm.edu	37	22	29885599	29885604	+	In_Frame_Del	DEL	AGGAAG	AGGAAG	-	rs267607534|rs373980795|rs267607533|rs149571560|rs200984527|rs370803228		TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	AGGAAG	AGGAAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr22:29885599_29885604delAGGAAG	ENST00000310624.6	+	4	2003_2008	c.1970_1975delAGGAAG	c.(1969-1977)aaggaagag>aag	p.EE658del		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	664	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						TCCCCAGAGAAGGAAGAGGCCAAGTC	0.558																																																	0			22																																								28215604	SO:0001651	inframe_deletion	4744				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1970_1975delAGGAAG	22.37:g.29885599_29885604delAGGAAG	ENSP00000311997:p.Glu658_Glu659del		28215599	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Del	DEL	ENST00000310624.6	37	CCDS13858.1																																																																																				0.558	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
ADM2	79924	hgsc.bcm.edu	37	22	50921149	50921166	+	In_Frame_Del	DEL	ACACTCGGGCCCCCGAAG	ACACTCGGGCCCCCGAAG	-	rs559809485|rs72438078|rs3840963|rs199649182	byFrequency	TCGA-AF-2693-01A-02D-1733-10	TCGA-AF-2693-10A-01D-1733-10	ACACTCGGGCCCCCGAAG	ACACTCGGGCCCCCGAAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	6a691061-ed35-414c-b69a-cb3a2aace286	7b486a6f-0922-4cf3-8076-78ad05b7e7a8	g.chr22:50921149_50921166delACACTCGGGCCCCCGAAG	ENST00000395738.2	+	2	556_573	c.264_281delACACTCGGGCCCCCGAAG	c.(262-282)caacactcgggcccccgaaga>caa	p.HSGPRR95del	ADM2_ENST00000362068.2_In_Frame_Del_p.TRAPED6del|ADM2_ENST00000395737.1_In_Frame_Del_p.HSGPRR95del	NM_001253845.1|NM_024866.5	NP_001240774.1|NP_079142.2	Q7Z4H4	ADM2_HUMAN	adrenomedullin 2	95					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|digestion (GO:0007586)|feeding behavior (GO:0007631)|negative regulation of blood pressure (GO:0045776)|positive regulation of angiogenesis (GO:0045766)|positive regulation of gene expression (GO:0010628)|protein phosphorylation (GO:0006468)	extracellular region (GO:0005576)	protein complex binding (GO:0032403)	p.H95_R100delHSGPRR(1)		breast(1)|kidney(1)	2		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GTGGCCGCCAACACTCGGGCCCCCGAAGACACTCGGGC	0.693														589	0.117612	0.0968	0.1686	5008	,	,		17047	0.1915		0.1213	False		,,,				2504	0.0297																1	Deletion - In frame(1)	breast(1)	22								288,3296		54,180,1558						2.4	0.0		dbSNP_130	10	572,6758		74,424,3167	no	coding	ADM2	NM_024866.4		128,604,4725	A1A1,A1R,RR		7.8035,8.0357,7.8798				860,10054				49268032	SO:0001651	inframe_deletion	79924			AF529213	CCDS33682.1	22q13.33	2013-02-25			ENSG00000128165	ENSG00000128165		"""Endogenous ligands"""	28898	protein-coding gene	gene with protein product		608682				14706825	Standard	NM_024866		Approved	AM2, FLJ21135	uc003blj.3	Q7Z4H4	OTTHUMG00000150202	ENST00000395738.2:c.264_281delACACTCGGGCCCCCGAAG	22.37:g.50921149_50921166delACACTCGGGCCCCCGAAG	ENSP00000379087:p.His95_Arg100del		49268015	Q3LFQ0	In_Frame_Del	DEL	ENST00000395738.2	37	CCDS33682.1																																																																																				0.693	ADM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316816.1	NM_024866	
